There are a ton of new and established breweries in and around there. Part will depend on how far you are willing to travel.
There isn't a lot right in Lowell at this point, Beer Works is pretty much it.
If you are willing to travel, it opens things way up. There is Riverwalk and Newburyport in Newburyport, Cape Ann in Gloucester,
Jack's Abby in Framingham, Greater Boston has Trillium (world class,) Harpoon, Sam Adams, Mystic (Everett) Aeronaut(Somerville) Cambridge Brewing Co (Cambridge - brewpub) Further out is Tree House in Monson (also world class; though an hour plus drive from Lowell)
in New Hampshire there are Throwback, Smuttymose, Earth Eagle, Portsmouth (brewpub) IncrediBREW, Martha's Exchange (brewpub) Border, among others.
Into Maine (also not far) you have Tributary, Allagash, Bissell Brothers, Austin Street and Foundation (those 4 are literally a stone's throw apart on one street in Portland) Maine Beer in Freeport, Gneiss in Limerick, along with several more in Portland area alone.
I don't know bottle shops in the Lowell area, but you should be able to find most of these, and many others, fairly easily.