In Midtown your only choice is
Joe: The Art of Coffee (beans from Barrington Roasters) in Grand Central Terminal. However, if you can make it to 20th Street and 7th Ave (at most, a 10 minute ride on the 1 train) to
Cafe Grumpy (their own Heartbreaker Espresso blend from Novo and a rotating guest espresso) you can try what some consider to be the best cafe on the island. Another amazing option is
Ninth Street Espresso (their own Alphabet City espresso blend roasted by Intelligentsia) in Chelsea Market on 15th Street and 9th Ave. Any of these three will give you delicious shots and should have a 1lb (or in the case of Grumpy, 12oz) bag of espresso available to take home. If you want to be picky you can call ahead and find out roast dates available.
For some reason I assumed that you're trapped on the west side: you should also check out
Everyman Espresso (Counter Culture's Espresso Toscano) at 13th Street between 3rd and 4th Ave for a delicious shot (beans should be available).
This blog post is an excellent reference for great cafes in Manhattan.
I haven't come close to listing everything. One more that I'll plug off the top of my head is
Kaffe 1668 (Intelligentsia Black Cat Classic and a rotating guest espresso) way downtown in Tribeca for an impressive cafe with two of everything (Synessos, Roburs, Clovers, etc.).
Good luck and let us know where you go!