Honduras and Nicaragua are both very inexpensive countries overall.
However, The Bay Islands are certainly more expensive than the Honduran mainland and Nicaragua. However, when compared to Belize and most other Caribbean destinations, they're on the inexpensive side. Overall, the islands (particularly Roatan and Utila) are touristy -- honestly, no part of the mainland (not even La Ceiba and Copan Valley) gets as many tourists as The Bay Islands. However, on Roatan, you can still get off the beaten path -- on The East End, you have access to Camp Bay (has the largest beach on the island), and learn about the culture by visiting places like Punta Gorda. Mangrove tours are also available.
The Bay Islands are nice, but take note that you'll use your wallet more at those islands than you would anywhere on the Honduran mainland and Nicaragua. Cruise ships do indeed stop by regularly -- but can be escaped.
I love both countries, by slight preference being Honduras, but I wouldn't choose The Bay Islands individually over Nicaragua.
As for the Caribbean cities in both countries, don't expect too much from the cities themselves.
La Ceiba itself isn't a particularly beautiful city (nor does its beaches compare to those of The Bay Islands), but in the surrounding area, you can hike at Pico Bonito National Park, visit Cuero y Salado Wildlife Refuge, and also go on other explorations in the surrounding areas. La Ceiba is one of the more popular spots of the mainland, but certainly doesn't get as much visits as most places in Costa Rica do. Tela is another notable spot in Honduras. The town itself is nothing special, but you can take a tour/explore natural areas such as Jeanette Kawas, Punta Izopo, and the Lancetilla Botanical Gardens. The beaches in front of town aren't very nice, but if you visit the surrounding Tela Bay, you'll find some nice beaches. Trujillo has very nice beaches, and is certainly not touristy.
As for Nicaragua, the main points of interest on the Caribbean are Bluefields (and surrounding area), and The Corn Islands. Aside from Bluefields, there aren't really any Caribbean towns of interest in Nicaragua (San Juan del Norte and Puerto Cabezas are interesting, but not offering much as of now).
IMO, the highlights of the countries are what you'll find on the mainland. La Ceiba, Tela, Copan Valley, and Lake Yojoa are great places in Honduras (The Lenca Trail is also great, but might be harder to do). Lake Nicaragua (including Ometepe) is amazing, and places like Granada, Leon, and Masaya are also great.
Nicaragua's Pacific beaches (especially near Leon) can get very nice), and there are also some nice beach spots on Honduras's North Coast. However, the countries have bigger fish to fry.
Question:
If you go to Honduras, are you planning to stay on The Bay Islands, or are you willing to explore parts of the mainland as well?
What places interest you in Nicaragua?
Both are beautiful countries, and surprisingly great in varied culture (both indigenous and non-indigenous), but I don't think the places you listed will give you a true taste of the countries.