Thor, beyond a shadow of a doubt. However, I am getting way, way ahead of myself. Before we get too far into 'who would win in a death battle,' we have to know what each one brings to the table as far as combat goes.

While I have seen Thor, I have not seen much of g1 Transformers (not even a full episode), so most of my Starscream knowledge has to come from somebody else. It just so happens that the information I am using comes from Death Battle, the episode where g1 Starscream fought against g4 Rainbow Dash, from My Little Pony, Friendship is Magic. and got crushed like a tin can He fought well, and provided the data I need for my argument. It also happens that Thor was also involved in a Death Battle, this time against Raiden from Mortal Combat. For the sake of being fair, I will use most of the points they raised in that battle for support, including his weaknesses, though most of my argument comes from the movies.

Let's start with Starscream, and run down his armor, weapons, and skill.
Starscream comes in two forms: F-15 Eagle fighter jet, and giant-frickin-robot. In his land based form, Starscream comes with an assortment of weapons, including:
Cluster bombs
Missiles
Machine guns
Some laser guns
Null-Ray: The Null-Ray focuses energy into a contained blast to shut down anything that runs on electricity. (How he did not manage to take over the Decepticons with this thing alone baffles me, but that's unimportant)
As a jet, his weaponry includes:
AIM homing missiles
-7F/M Sparrows
-120 AMRAAM Slammers
-9L/M Sidewinders
M61A1 Vulcan gatling gun
I have little idea of what these truly are, but from what I have gleamed, the three missiles are basically different ranges. In order as presented above: Mid-range, long-range, short-range. The gatling gun shoots really, really fast. It's rather good. Not much else to say on it.

Starscream can fly, either over short distances in his robot form, or long-ranges in his jet form. As a jet, he can fly at top speeds of Mach 2.5+ or 1,650+ mph.

Starscream likes to think of himself as a strategist, though several of his plans fail. Miserably. Despite this, he does have a way with words, and manages to be just competent enough to stay as one of the higher-ranking officials. He is fond of stabbing people in the back and utilizing the element of surprise. That said, he is also headstrong, so his idea of 'surprise' is often "charge in front of the enemy, fein damage and inhabitation, then shoot them when they least expect it." This makes his Null-Ray more effective, as it seems to work best at close distances. This may be because Starscream is a horrid shot. There is a reason his missiles are tracking.

Now let's cover Thor.
Thor is the Norse god of thunder, giving him mastery over storms and lightning. His weaponry includes:
Lightning bolts
Thunder blasts
Vortexes
Storms
Mjolnir

Mjolnir is Thor's signature weapon. This one handed hammer, forged by the dwarves as an ultimate gift, can perform a variety of attacks. When the dwarves gave the hammer to Thor, they described it as such: "Thor might smite as hard as he desired, whatsoever might be before him, and the hammer would not fail; and if he threw it at anything, it would never miss, and never fly so far as not to return to his hand; and if be desired, he might keep it in his sark, it was so small; but indeed it was a flaw in the hammer that the fore-haft was somewhat short." Beyond these powers, it seems to be a conduit for Thor's energy. He can send lightning bolts out of the head, call forth his armor, and even fly after spinning the hammer in his hand really fast. It has also been known in the comics to control electro-magnetic fields, though this ability has not been shown in the movies yet.

Thor is a mountain of a man, as well as a god. His skin is neigh invulnerable, though he can be damaged if enough force is applied. Thor has had numerous fights with the Hulk, one of the strongest and hardest hitting things in the universe, and has escaped with only a few bruises. Even though his hammer carries most of his strength inside of it, Thor is no weakling himself. He among the strongest of the Asgardians, and as stated before, has traded blows with the Hulk, one of the few beings that can be stronger then him.

So, now it comes down to this. Who would win? As I said in the beginning, Thor would not only win, but annihilate Starscream.

Starscream's best weapon, the Null-Ray, is completely useless against organic beings, which Thor is. The rest of his arsenal, while it may be able to damage Thor if he concentrated almost all of his firepower onto the god at once, but even then it seems unlikely. Starscream's best chance is to grab Thor in a bear hug and transform into a jet as soon as he could, crushing Thor in the process. Of corse, that would probably only allow the god to rip him apart from the inside.

Thor on the other hand has a much greater offensive capability. All electrical systems can be overpowered, and several bolts of lightning should overcharge any robot, no matter how advanced their technology is. Should Starscream attempt to fly away, Thor could easily catch up to him, using his hammer to fly up to the jet. Once close enough to Starscream to hit, Mjolnir would be more then strong enough to tear right through him. In fact, Thor does not even need to be close to hit, as he has shown remarkable throwing capabilities with his hammer. Finaly, should Starscream manage to fly far enough away that Thor could not catch him, the god of thunder could call in a vortex to rip Starscream's body apart with lightning and extraordinarily heavy wind.

The winner is Thor.