wishing we still had:
Bass NW
The Perfect Bass
Atlanta Bass Gallery
I'd add Bass Specialties to the "wish we still had" list. What an awesome place that was, and I could get there in 25 minutes from home. I had great experiences buying a custom order G&L JB and an Epifani cab there, and it was a fantastic place to sell stuff on consignment. Glenn is a really great dude, and I hope he's doing well.
In New Jersey, you could check out New Jersey Guitar and Bass Center:
http://newjerseyguitarandbasscenter.com. Jay always has interesting stuff, and he's a really nice guy. Prices aren't great, but you'll pay less if you pay in cash.
Also in Jersey, Kebo's Bass Works:
Kebos Bass Works. I've never been to the shop, but I've checked out their stuff at the Philly area guitar show. They have some very nice and interesting basses, which last year included some inventory they acquired out of the Atlanta Bass Gallery closure. But IIRC, their prices were on the high side.
In Philly, there's Roxy Guitar (
Link Removed), which has very limited hours and, historically at least, has not carried many basses. But if you're into Warrior stuff, this is the place, and they do sell used gear so you never know what they'll have. Falls into the "worth calling if you'll be in the area" category, but not worth going out of your way -- unless, that is, you're also afflicted with guitar GAS, in which case it's a must-visit. The guitar selection is unbelievable, as is the selection of guitar amps.