Well defnitely you will have to do Granada for at leats 2 nights. I recommend the following:
Day 1: Managua Airport to Granada - City tour Granada and the Isletas tour.
Day 2: Masaya Volcano, Masaya`s market, Catarina and San Juan de Oriente.
Day 3: Ometepe 1 day tour, after tour spend the night in San Juan del Sur.
Day 4: Free in San Juan del Sur
Day 5: San Juan del Sur - Managua.
I will recommend an early flight to Managua in order to do the Granada activities. Please do not hesiate to contact me for anuything that you may need at firstname.lastname@example.org
I was in Nicaragua about a month ago for a few weeks and Isla de Ometepe was one of my favorite places. I spent about a week there and about a week in Granada. I couldn't personally imagine trying to fit in all three of those destinations in 5 days, but it depends on what your traveling style is like. I would say you need more than a day trip to Ometepe, but it depends what you are looking for. I didn't go to SJDS, but I've heard it has great beaches and is mainly a surfer town. Ometepe is beautiful and has a lot of great hiking. There are two volcanoes to climb (each take about a full day), otherwise I recommend going to the San Ramon waterfall which can be done in a half day. Then jumping in Lake Nicaragua after your hike is a great way to end the evening.
I second the recommendation of checking out the Masaya Volcano from Granada. Do a tour of the lava tubes, and you get to wear gas masks! On a side note, if you find yourself in Granada during the weekend and you enjoy going out dancing, I recommend going to Cafe Nuit!
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