As a Boston guy here is your answer: Yes he will be welcomed here. Eli did not win either of those games by dominating our defense. He played very well in both games, but it was insane catches(Tyree, Manningham) coupled with rare drops by Welker, Hernandez and Branch(or in 2007 by Asante Samuel, which would have made Eli not welcome in NY). the one that hurts the most is Welker's drop which could have been the play that changed the game. Either way the Giants work hard and play hard, and got the win, Congrats to them. Their fans don't come close to Yankees fans in the way they handle themselves. Giants fans don't talk trash by referencing championships won before they were born. The arrogance of Yankees fans(similar to Red sox fans) can be infuriating not on a rival team level, but on a human level.
There is your answer now and take these conversations to the Pro Sports board so i don't have to avoid this site for the next two weeks.