I recently picked up a great "board game" that is co-op: Shadowrift It is actually a co-op deckbuilding card game, similar to Dominion. Only, it has a lot more theme and is co-op.
My wife and I have played it two player and is a lot of fun. It *can* be difficult with only 2 players, though. Some of the monster decks are pretty tough (it comes with 8 monster decks, I think, and we've played against 3 of them so far). We've been thinking of playing two hands each, but haven't tried that yet.
Pandemic is good with 2 players. So is Eldritch Horror, and isn't quite as long as Arkham Horror (Arkham Horror is good 2-player as well)
Sentinels of the Multi-verse is good 2-player, but there is a minimum of 3 heroes, so either one or both of you will need to play a second hero. My wife and I typically play 2 heroes each, alternating hero turns (mine, hers, mine, hers, for example), and it works just fine.