I'm not aware of any ferry service between El Salvador and Costa Rica, and I cover both countries for a large guidebook publisher. That doesn't mean the service doesn't exist, but I've never heard of it.
I see that flying with Taca is going to be in the low $300s round trip, as long as you don't fly on the Friday-Saturday-Sundays bracketing Holy Week. Then it seems to shoot to $400-500. That takes you to San Jose, which is nowhere near the Nicaraguan border. (If you've never been to Costa Rica, you'll see that the highway system is nowhere as good as it is in El Salvador.) Even if you're already in far northern Costa Rica, a day trip to Nicaragua is difficult to do on your own.