"we were kind of surprised that there weren't any marina's or moorings available along NYC! "
If you mean Manhattan? North Cove, the marina at the World Trade Center, should still be taking guests. Try not to flinch at the prices. On the East River side, the South Street Seaport Museum also used to take guests with a discount for members. Further up the next stops would be the 34th Street marinas, never asked about transient slips but I'd still expect the prices to be steep. Further up the East River you can anchor for free in the coves northeast of Roosevelt Island, although your anchor might not come up again afterwards. Hallets Cove and Pots Cove both were marked anchorages last time I checked. Not Kodak Picture Spots but...if you need to wait out the current at Hell Gate northbound, at least they are there.
The waterside real estate is just a bit expensive for casual boaters. Slim pickings if your boat isn't 100' OAL with a helipad on the stern.