If you're considering looking at used gear, I'd also recommend
Rogue Music. It's on 30th right across the street from 30th St. guitars. Their selection is eclectic, but they're about as fairly priced as I've seen in NY and they can be expected to have one or two very good items when you go in there. The staff is also better than anything I've seen in a chain store - that is they know something about the gear they're selling and they don't upsell you.
If, however, you're just looking for a particular new model product that Sam Ash/Manny's and Guitar Center both have in stock, you might as well figure out what both of them are selling it for and haggle them against one another. Unless one of them is running some sort of promo deal with Gibson, the difference will probably come down to something like $10, a bag or Tortex picks or "this sweet new cord from Monster". Go for the picks.
I don't like shopping at these stores for personal reasons. If you do go the used route, avoid just wandering into some Village place just because it's selling guitars. Those places are for Japanese tourists, ex-Hit Factory session musicians and Hard Rock Cafe yuppies. You'll get ripped off.
And on Tuesday, you can see the Wu-Tang Clan and wish Inspectah Deck a Happy Valentine's Day. NYC has everything.
= Justin