listen to nruva, he knows his shit.
Goodtimes is where you want to go. There are definitely a few problems with the place (kinda ghetto area, kid got killed there a few months ago, shitty upkeep of the machines), but like nruva said, they have a lot of games. There's good variety too: schmups (Raiden Fighters Jet woot!), Slugs, a couple KOF's including 2003, Wangan Midnight and Initial D, all the old school dedicated cabs you could want, and much much more. And yes, they have Third Strike. And double yes, they serve beer. Oh wait, you didn't ask about that...
It's actually in Somerville, not BOston, but it's super-close. Their home is
http://www.goodtimeemporium.com/ and you can get directions depending on which way you are coming from on Rt. 93.
If you need any other directions or have questions, you can always post here or PM me. Have fun, man!