We booked packages for both Mato Grosso and Moto Grosso do Sul onltine through Brazil Nature Tours based in Campo Grande. They arranged both our Pantanal packages, although we booked our own flights. They did a great job. I am sure you can find something in your price range with them.
In Mato Grosso, we stayed at Jaguar Ecological Reserve on the Transpantaneira Highway. It was a rustic, simple family-owned place with simple accommodations and food. it was not cheap, but the isolated, serene location was amazing--we were in the thick of things, and Eduardo, the owner/guide is highly experienced. We stayed three nights and saw heaps of wildlife, particularly birds, caiman, and capybara. You are surrounded by wildlife. Sadly, we saw no jaguars, just tracks, and no giant otters, but we went early in the season. Because of flight schedules, you might be obliged to spend the night in Cuiaba, four hours drive away.
In Mato Grosso do Sul, we stayed at Caiman Ecological Refuge, three or four hours drive from Campo Grande. A beautiful place with excellent accommodations and great food. It is part of a large working ranch. Saw loads of wildlife here, too, but not as much as on the Transpantaneira Highway/Mato Grosso. We also road horses through the wetlands (bring old shoes as they will get muddy). We stayed in their Baiazinha lodge, which faces a small lake. We'd love to go back there.
We did boat trips at both Jaguar Ecological Reserve and Caiman Ecological Refuge.
There are many great fazendas you can stay at in the Pantanal.
Don't go to the Pantanal in November, this will be the start of wet season.