MGA>Masaya/Granada
Yes you can get to Masaya from MGA airport at night, just hire a taxi. Make sure your lodging in Masaya or Granada know your arriving late and give them the time. Even better have them send a driver to meet you.
Greytown/Bluefields Boats
It is no problem going from San Carlos/Rio San Juan to Greytown and onward to Bluefields. Boats are running.
Be sure to explore the Biospheres at El Castillo area. You can also take a bus from Managua to Rama, then take boats...
Nicaragua Beaches
I would not even bother going to San Juan Del sur, and focus on the Corn Islands and Las Penitas. SJDS is a tourist/backpacker ghetto that makes Vieng Vang Laos look good. (SE Asia). If you do go, be aware of the Bed Bug Issues in the hostels and low end lodging. You also can't swim off the town beach, and you need to commute to the nice beaches.
You can shuttle from Leon to Antigua...a very long ride, but possible to save time and hassle.
Honduras/Bay Islands/Utila
Its a great place to go scuba diving, though Utila is not really known for its beaches, it is known for having the second longest reef in the world, and being a great and inexpensive option for getting your PADI Open Water Diving Certification, $300 includes dorm lodging on Utila. Plan 5-6 days for this jaunt.
Getting there is not fast nor on the way to anything or anywhere, so you need to get a bus or shuttle to San Pedro Sula, then a bus to La Cieba, and then the ferry to Utila (morning and late afternoon). You also can fly from SPS to Utila, or Roatan, which has a nicer beach in West Bay, though its more touristy, I prefer to West End..and Halfmoon Bay.
Honduras/El Salvador
You also can take a boat from Potosi Nicaragua, to La Union El Salvador, which then puts you just south of the surf beaches in and around Playa El Tunco. From there you can shuttle to Guatemala City/Antigua, bypassing Honduras all together, and the major cities. (Best avoided).
Guatemala/Tikal
I would nip Tikal in the bud and go there via overnight bus from GC or Antigua, or fly from GC to Flores, and then shuttle or local van to El Ramente and Flores. Depending on time, you may want to consider breaking up the return trip to GC/Antigua via Lanquin/Copan a few nights. Or Vice versa from Antigua/GC to Flores.
Lake Atitlan is a pretty special place and relaxing too, you get around via boats to the various indigenous lakeside villages. Plan at least 4 nights around the lake.
Nature/Wildlife/Beaches
If you are not into culture, and seeking beaches and nature/wildlife and Bio Diversity, you really should head to Costa Rica, as it has the best beaches on both coast, in CA, it also has a plethora of National Parks and excellent eco systems and a wide variety of Bio Diversity and unique landscapes, rainforest, jungle, rivers, lakes, volcanoes, mangroves, waterfalls, marine refuges, pine forest, dry forest, cloud forest, canals galore. The beach and surf/party scene is also a mecca for fun and the younger crowd.
Overview
Nicaragua, El Salvador and for Guatemala, is not known for its beaches in comparison, other than its surf. But Guatemala is the cultural gem of the region, and is well worth 3 weeks of exploring, it also has a lot of great hiking/volcanoes to access, even as overnights...love Guatamala....
Just saying....