What are the ways of improving water tiles?

Solution 1:

• Tile Improvements: Work boats can be used to develop special resource tiles on water (like fish, whale, and oil).
• Wonders: As mentioned, the Colossus of Rhodes increases commerce.
• Social Policies: Merchant Navy (Commerce) helps somewhat indirectly, by giving +3 production in coastal cities.
• Buildings: As mentioned in the question, the Seaport and Lighthouse improve output of water tiles.
• Technologies: I believe as you get higher technologies, the output of water tiles will be improved as well. EDIT: I think I was mistaken about this (unfortunately can't load the game up at work).

Solution 2:

The Seaport adds +2 hammers to ocean tiles that have resources. It's an excellent option for cities with several ocean resources tiles it can work. It's a mid-game structure (at earliest), though.