San Carlos is an overnight boat trip from Ometepe (schedules on vianica.com, unter Ometepe), and from there there are speed and slow boats running downstream to Boca de Sabalos (not much there), El Castillo (quaint little town with an impressive Spanish fortress and great history - check vianica.com for details) and all the way down to San Juan del Norte (great little village with huge history - do some research on the Vanderbilt shipping lines during the Gold Rush, Greytown, etc. and you'll be hooked.)
El Castillo is roughly 2 hours, SJDN 6 hours by speed boat and 12 hrs by slow boat from San Carlos. Obviously you can always hire private river transport and do everything at yout own pace.
It goes without saying (so I hope) that you can't compare Corn Island and the river. What is there to do? Other than the historical sites, there's the biggest jungkle reserve in the country in the shape of Indio Maiz reserve, which has a few trails that can be easily done at Bartola (6 km downstream from El Castillo, great lodge to stay and relax, pricy at 50 USD meals included but worth it) and a more difficult access leaving from SJDN. But if the weather is crap on the Corn Islands, it will in all likeliness be worse at SJDN.
Oh, and if you're into fishing, there's quite a few fishing lodges between San Carlos and El Castillo. Never been to either of them, so can't say much. May if you do some research on Montecristo or Sabalos lodge (two names that spring to mind) you'll come up with something.
Do some research on the river here on these pages too, and you'll find some interesting stuff.
