It would be extremely helpful if there was some way to get an extra unit of food from those water tiles. Is there some thing that I'm missing that I can do to get extra food from them, or am I stuck with the (almost) worthless 2 food and 2 gold?

Lighthouse = +1 food on water tiles.

I think he emans with lighthouse. Only way is with a special resource :/ 2 food and 2 commerce isnt worthless because your city will grow from 2 food if its healthy. It will become a financial center.

there is one trick

basicly you get 1 food from sea
and 2 food from lake

you can built lighthouse only if the city is next to sea
but if the city has in its radius both sea and lake it can build lighthouse and have 3 food from lake ;)

^Somehow I don't think that works...
That's been thoroughly corrected.

Yes, it does.
http://www.civfanatics.net/uploads10/rb1-38.jpg

This screenshot is taken from the Cuban Isolationists thread. It's a fantastic read.
http://forums.civfanatics.com/showthread.php?t=133492