It's been my general observation that currents in the bay have a counter clockwise tendency, substantially because ebb tide outflow through First Narrows acts as a jet, like a giant garden hose that's used to induce rotating flow into a wading pool. Consequently, the eastward flow past Spanish Banks is much stronger during flood tide than the westward flow is during ebb. In fact, the eastward flow tends to continue well into an ebb tide.
The foregoing is a general pattern. That said, any substantial eastward flow is countered by a westward-ish eddy close to shore, especially downstream of the (exposed or submerged) Spanish Banks sandbars. It's particularly notable immediately westward of the Jericho pier. That's why sailboat races over the years have tended to be won by sailors who tack closest to shore when sailing westward. The effect is usually dramatic, and not necessarily only during a flood tide.
Yesterday I noticed something interesting while I was on the Jericho pier, about three quarters of the way through a substantial flood tide. Water was flowing westward past the pier at about a full knot. This is consistent with my longtime eddy observations, but much more significant than I'd expected. I'm curious how far out that westward eddy extends. Any insight?