Okay, here's my observations on San Juan. I hope this helps some...
I actually stayed at Hotel Colonial (http://www.hotel-nicaragua.com)
. The people were pretty friendly, though spoke little English. The good is that the rooms were clean and reasonably comfortable, if basic. A/C worked well, plus the room had a ceiling fan. Note if you need heavier blankets at night, the bed really only has sheets and they didn't seem to have anything heavier than another sheet. My room, #5, was a queen size bed (I think) and there wasn't a lot of additional room, but did have an armoire and desk. I did see other bed options in other rooms. The TV was on the desk, and does have cable to include New York stations and English Central American stations. Bathroom was reasonably modern. I would compare it a lot to a Days Inn or similar (though a little cleaner than some Days Inn's I've seen). Rate for me was $45/night including tax and continental breakfast (eggs and such available for a buck or two). The hotel is right in town and only a block from the bay, so pretty convenient. Downsides: a couple of ants made their way into the room (nothing overwhelming, but a few). Other bigger concern is they seem to have power trips. At first I thought it was just the power problems I have observed of Nicaragua but later realized it was only the hotel that had no power. It seemed to be turned back on within a few minutes when they turned it back on. You might want to inquire on that, or if you stay here make sure you're asking if you lose power in the room.
I also looked at Hotel Victoriano(http://www.hotelvictoriano.com/)
. I actually looked at the rooms, and they were quite nice. Everything you'd pretty much expect in a nicer U.S. hotel: A/C, nice decor, cable, security boxes, etc. Now, they did quote a fairly high price at $100-115/night. That said, maybe if you contacted them and asked about a weekly rate they could do something for you. This one is on the bay and near everything else in town.
I also saw two others from the outside. I didn't get the opportunity to look inside, but both looked nice and seem worth at least checking out: Casa Marina(http://www.sanjuandelsur.org.ni/hotels/luxury/casamarina.html)
. This is not their exact website that was on the side of the hotel, but I don't remember it and didn't find it in a Google search. Finally, there is Inn on the Pacific (http://www.innonthepacific.net).
. I personally found their website a little annoying as I didn't see a way to turn off the music, but looks nice from the outside and on the bay too. Their rates looked to be a little on the higher end of your budget at $80-125.
I hope that is of some help for you, R. There are a number of other hotels to explore, many of them small and more basic. Let me know if you have other questions.
Darren, I will still let you know if I make it to Leon or gather information, but keep looking for alternate information. I am thinking I may not make it there this time around. I'm sorry about that...have you thought about seeing if there's a church in Leon you can contact? Perhaps they would have a parishioner that would entertain a homestay? Just a thought...