I can't speak for any of the on-line coures, but the Coast Guard Aux and US Power Squadrons have excellent programs.
With USPS, I have taken the Basic Squadron Boating Course. Seamanship, Piloting, Advanced Piloting, and the GPS & Weather seminars. For piloting, you start with chart, dividers, plotter, calculator and learn how to do it the old fashioned way (i.e.,how you would have to do it when (not if) your gps, etc., crap out or get hit by lightining.
If you are truly adventurous, you can continue with Junior Navigation and Navigation. The is based on using a sextant and the star chart tables and is intended for offshore blue water cruising.
A good companion book to the Advanced Piloting course is the Weekend Navigator by Bob Sweet. This book also includes (or did when I got it) Maptech software which is easy to use but not on my 64 bit laptop.
Hope this is helpful.
Kim Boyer
USPS AP