You can get them at Katagiri. I wouldn't be surprised if Sunrise Mart also had them. There is a farmer that sells plants at the USQ greenmarket which I purchased in May and which is now fruiting beautifully.
4 Stuyvesant St, New York, NY 10003
224 E 59th St, New York, NY 10022
I've had it at ABC Kitchen, which buys it from the Union Sq. greenmarket. I've also eaten shishitos at Little Giant in the LES.
I've bought shisitos from:
1) Norwich Meadow Farms
2) Lan's farms (only there on Mondays)
85 Orchard Street, New York, NY 10002
35 E 18th St, New York, NY 10003
Union Square Greenmarket is where I go, too, usually at Lani's Farm or Bodhitree. BTW, Lani's Farm and Bodhitree used to be Yuno's Farm but they split up.
Shisito peppers are in season right now, and not for long....
Lani's Farm schedule:
Monday: Union Square Greenmarket
Wednesday: Dag Hammarskjold & Tribeca
Sunday: Carroll Gardens
Wednesday and Friday: Union Square
Saturday: Abingdon Square
I'm not sure where they are on other days, if they're in the city at all.
Union Square Greenmarket
Broadway and E 17th St, New York, NY 10003