Posting mostly to follow. I'm in Harlem, too. We buy a lot of our staples (big things of walnuts and oatmeal, for example) at the east Harlem Costco complex, buy perishable staples at the shady local grocer, and then make outings to Fairway or Trader Joe's or Best Yet on 120 (we're further south) for more interesting stuff. If you're near the 1/2/3, you can make the Trader Joe's and ~98th Street fairway run pretty efficient, especially on weekend mornings or off times.
Does the East Harlem Costco have good prices on produce/meat/brand name items as well? Because of kiddo's allergies, we can buy some Kirkland brand items but for other staple/packaged things we have to go for specific safe brands (she has one safe brand of pasta, two safe brands of rice, two safe brands of oatmeal, etc).
I think we need to suss out the less crazy times for that Upper West Side Trader Joe's -- it's along my evening subway ride home on the 1, but that always seems to be the worst time to go.
We've been going to the Fairway on the water near 132nd because it's close biking/walking distance but the prices doesn't seem like as much of a savings over Key Food as they were in our Brooklyn Fairway.
I hadn't heard of Best Yet!
I'm probably the worst person to ask about the Costco offerings because we're only two people with a very tiny fridge so we don't really get produce there (it goes bad), we don't eat meat, and we don't have brand-specific requirements.
Best Yet is actually now called Best Market (2187 FDB). I'm not sure it is better than Fairway, I think if I were closer to Fairway (I'm between 6th and 7th), I would probably go there, instead. I haven't really priced them against each other, but think of them as relatively equivalent and go to whichever one is easier.
Uptown is generally underserved by supermarkets, and it seems like a lot of them have an old-school paper circular system for coupons, which I don't really think is worth my time, honestly. Fairway and Best Market have more modern coupon systems where you can sign up for email discounts, etc.
I am a fan of the TJ/Fairway combo run on the UWS, although now that I'm 35 weeks pregnant, I'm pretty useless for food shopping for more than a bag at a time. It can take some time, but I don't find standing on the subway with bags all that stressful if I'm not on my way to an appointment. My husband's preferred method is to make repeated runs to the local place, which may not be as workable of a strategy with a newborn...
Not sure what neighborhood you work in, but you could check out grocery options there, as well.
One last idea: for non-perishables/diapers/cleaning supplies/etc, see what you can get on Amazon, assuming you have a doorman. Then you're just shopping for fresh stuff.