I'm gonna go ahead and disagree and say that Martha's is terrible, please don't waste your time there. Nashua has its own dedicated beer store now (called... The Beer Store) but there's very little distributed in NH compared to MA. If you're up for a hike Julios in Westborough is one of the best shops around, but if you're driving that far you might as well hit up some of the great beer bars in/around Boston instead. Sorry, since I don't spend a lot of time there I don't know of any shops in Lowell. There's an OK one in Tyngsboro near the NH border but I remember it being pretty pricey.
If you really want to make it a good beer trip, plan to spend a day barhopping in Boston. Or else drive up to Novare Res in Portland ME, or head to the Portsmouth Brewery/Smuttynose in Portsmouth. Jack's Abby in Framingham is also great, though I haven't visited the brewery yet.