Daniel,
There are a few sites that sell bulk LEDs but you want to make sure you meet the CG's 2 nautical mile requirement before you go out at night.
Here is a link to Annex I - 33 CFR Part 84 (POSITIONING AND TECHNICAL DETAILS OF LIGHTS AND SHAPES)
http://www.access.gpo.gov/nara/cfr/wais ... 84_04.html
That should help you in designing your housings.
Superbrightleds.com sells many types of LEDs including 360 degree leds with a phosphorescent coating and 1 Watt square base LEDs. I've purchased from them before and always had great service.
If you are also looking to make cabin lights, don't forget to pick a color that is pleasing to the eye at night and seal them in epoxy after you make all connections at the "bulb" (since trailering can induce loads of vibration on the boat).
I too was looking a replacing my 60's era Perko navigation lamps after the boat is finished (which is taking much longer then I expected), and can't believe the prices of LED hardware.
Hope this helps in your quest!
Marc
DS1 2902