Courtesy of Stevens Institute in NJ:
Scroll through a couple of times to get a feel for how the currents work.
Also, check out ActiveCaptain.com
for anchorages if you think you want to wait out the current. Good ones include Little Bay (under the Throgs Neck Bridge) before heading down the East River and between the Statue of Liberty and Ellis Island (watch for well-marked security zones) before heading up the Hudson River.