I used to sail out of Alameda Marina (a couple more miles up the Oakland-Alameda Estuary from JL Square), so I've had some experience with the wind and currents you're likely to encounter. Most of the little tide books you can get at marine stores, bait shops, et cetera, will have current info and time off-sets toward the back. Also, you can use "Mr. Tides" on a Mac, but I don't know if there is an iPad version. The tidal flow in the Estuary can be a bit frustrating on a calm day, particularly along the stretch from JLS to Middle Harbor. However, since the afternoon winds almost always blow from SF Bay proper into the Estuary it would have to be a heck of an ebb to keep you from getting back to JLS. Having said that, I did get caught by a HUGE ebb one evening as I was trying to get back from Gashouse Cove to Alameda (I sat almost stationary off Pier 39, fighting the ebb, for what seemed like hours). By the time I got back into the Estuary the wind had died, but tide had finally started to turn and I more or less drifted back to Alameda Marina.
As for day trips from JLS, South Beach Marina or Central Basin are both easy daysails. Pier 39 and SF Aquatic Park are also well within range. Tiburon, Angel Island, or Sausalito will take a bit longer, but fine if you're game for a long day. The great advantage you have is that the Estuary is usually downwind from the Central Bay, so your return trip should be a nice run. Just watch out for them big ol' container ships.
Never forget them. Do something to prevent it from happening again.
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