I'll second for Barcade, simply amazing place! A holy mecca of classic arcade gaming that everyone should visit.

Awesome beer on tap as well.. and a tapper machine to make it all the more fun!

If you are in Manhattan there is a good but kinda shady arcade in China Town on Doyers St. off Bowery. They have brand new games like Tekken 6, SF IV, Blaz Blue in fancy new LCD sit down cabs, although none of them seem legit but rather knock off cabs from china. Theres also plenty of good 90s uprights to play too. I noticed I was watched quite closely by some guys at the door because i didn't stay to play anything. I was told its a chinese mob run business just like most of the gift shops in china town are. It was pretty busy anyway.
Another place in Manhattan that had all you can play galaga and ms pacman cocktails was a cool bar called "675 Bar"
http://www.thrillist.com/meatpacking-district/675-barIf you are looking to play some classic real "Skee-ball" at $1.00 a game, you can go to Ace Bar. They also have a CSI pin and a few games, pool tables and real darts.
http://www.acebar.com/