Ecuador's top two destinations for cruising boats are Bahia de Caraquez along the coast toward the Colombian border; and Puerto Lucia, the marina nestled between the towns of La Libertad and Salinas and just east of Punta Santa Elena, South America's westernmost point. Find the Galapagos Islands on a map and draw a line due east toward the Ecuadorean mainland and look for a pointy pice of land sticking out to the west: that's about where Punta Santa Elena and Puerto Lucia are.
We have not (yet) visited Bahia de Caraquez so I can only report that the folks we've met who have been there have said they've generally enjoyed it, and felt their boats were safe enough at anchor or on a mooring (Bahia's only two options for now) to travel away from them for weeks at a time. They say there's a fellow in Bahia you can hire to watch your boat, and they've said their boats have all been fine upon their return. We hear the official Ecuadorean entry/exit paperwork in Bahia is totally do-it-yourself; I don't know what the fees are but they're undoubtedly much cheaper than using an agent like we were required to do when we entered at Puerto Lucia. It seems that more cruisers who sail to Ecuador stop at Bahia rather than Puerto Lucia - I'm guessing because it's cheaper. So, why then did we choose to travel 120 miles further southand west, and pay larger coin, to stay for 5-1/2 months at Puerto Lucia?
Because we intended to do a lot of inland travel and wanted a secure place to leave our boat, plus quick and easy access to long-range transportation. Puerto Lucia has all that: it's a gated resort/marina with 24/7 security and lots of amenities; plus, it's only a 2-1/2 hour, first-class, $3.50 bus ride from La Libertad to Guayaquil, Ecuador's largest city. Guayaquil's an excellent bus and airport hub for getting to the rest of Ecuador, South America and beyond. Buses leave La Libertad for Guayaquil every 8 minutes during the day, and there are many taxi/charter van options if for whatever reason you can't take a bus. Puerto Lucia also boasts Ecuador's only boat yard so if something goes kerflooey on your boat between Panama and the Galapagos, you'll be putting in here whether you want to or not.
Following are other pluses and minuses of having a boat at Puerto Lucia. First, the minuses: