Sylar was the bomb the first time. Future Hiro was there.
Saving Claire did change some other things, too. If Sylar had killed her, Bennett would not have tried to betray the Company by helping her escape. Which is what got him locked up. Which is why he's now helping Ted get to New York. Claire's being alive is also the reason that the Haitian ran away from the company.
Anyway... in the original timeline, things happened as Future Hiro said. Sylar started to explode. Hiro stabbed him. As soon as the sword was removed, Sylar regenerated and exploded. (Hiro must have teleported out at the last second.)
Hiro did some research. He found out that the regenerating power came from Claire, and that Peter was on the subway when the power went out. He went back and told Peter to save Claire, figuring that the only major change this would create would be to remove Sylar's ability to regenerate. So that when Hiro stabbed him, he'd die.
But, as mentioned, there were other changes. Now, Peter is the bomb. But very few people know that because Nathan covered it up. (And then, later, Sylar gained Candace's power, killed Nathan, and took his place.) Basically, many of the changes made by saving Claire canceled each other out.
As for why either Sylar or Peter would explode... I'm wondering if it might have something to do with that little girl from next week's preview. Bennett's old boss says that "she's the only one who can stop Sylar," but his boss is Linderman... and Linderman wants the bomb to happen.
So maybe her ability is the power to disrupt other people's powers. Make them lose control. And they're going to use her as a weapon against Sylar. Only she runs into Peter by mistake. Who, having run into Ted, has a new power that he doesn't know how to control. He starts to explode, Hiro comes in (having been told that he needs to stop the explosion), Peter gets stabbed through the chest, the explosion is averted, and then Peter regenerates when the sword is removed.
Or something like that.
We'll see, I guess.
