I've also seen them recently at Trader Joe's in Queens, and would assume they would have them in Manhattan as well, but they looked a bit past their prime.
I saw them bagged in Whole Foods and loose in Fairway. In Fairway the sign called them "sweet lemons" but the sticker said "meyer lemons." I believe they were $3.89/lb in Fairway.
I've purchased them at Gourmet Garage, but I haven't seen them there for a while. Might try Garden of Eden too. But as Kathryn mentioned maybe the season is over...
That is my sense as well - haven't seen them for awhile. Eli's is my "go to" place for produce that is out of season - maybe worth calling, though it's on the UES.