For Selection, Shoreline in Huntington is by far the best. Very organized and the growlers change often.
For price, I'd go with Bullseye in Smithtown. Very friendly staff as well.
On a side note, i've been going to the new Whole Foods in Lake Grove a lot lately. They have the best beer selection for a grocery store, although it's a bit pricey. They have 4-5 growler choices which are actually priced well. You can get a 32oz for $4-6 and a 64oz for $8-11. Mostly local stuff.
They have a 10% discount if you are a member of the B.E.E.R club (Brewers East End Revival Club; $20 yearly membership). Also, since there are multiple locations....their prices and selection are pretty good!!
You may also wish to check out Bellport Beverage.....Say "Hi to Bellport Dave. They have a nice selection and knowledgable staff.