Rurrenabaque tours

Just book the day before (or even the morning of) you want to go. There are a ton of tour operators and there is a chance that even if you book with one you will end up with a different operator because yours couldn't fill a group. I used Amazonia and was happy with them. I also highly recommend Cafe Pirana for breakfast -- they serve delicious croisants!

Yes, normally it is best and easiest to book in Rurrenabaque. All the tour operators have offices in Rurrenabaque, and you can compare the possibilities. Also you may risk delays on the flight, and you cannot be sure to arrive the planned day.
You can choose between jungle and pampas tours, and for the pampas tours your choice may depend on your attitude to touching and feeding wild animals.

The jungle/rainforest is south and west of Rurrenabaque (inclusive a part of the Madidi National Park), and the tours go by boat and foot.
The pampas tours go to the area of the Yacuma River, north east of Rurrenabaque and Reyes, and the tours start with a long drive. The road is likely to be either wet or bumpy after having dried up with deep wheel tracks in the mud.

About investigation beforehand: Try a search here at the Thorn Tree for: Rurrenabaque tour (With plus signs)
(The Thorn Tree Help tells more about the search function).
Do another search for: Rurrenabaque tours (With s in tours).

More information about Rurrenabaque and tours: http://wikitravel.org/en/Rurrenabaque and http://en.wikipedia.org/wiki/Rurrenabaque

About flying La Paz - Rurrenabaque search here at TT for: flight Rurrenabaque
Two airlines fly the route: Línea Aérea Amaszonas at http://www.amaszonas.com and Transporte Aéreo Militar = TAM (Not to be mixed up with the Brazilian TAM Linhas Aéreas).
Be aware of the difficulties of flying to and from Rurre. Delays and cancellations may be frequent, as told in many threads here at TT. Have a flexible itinerary.
Rurrenabaque and the surrounding rainforest and pampas are wonderful and worth the trouble.

Other sources are of course guidebooks. The Lonely Planet Bolivia guidebook is also available in downloadable individual chapters.

The LP Bolivia guide, 6th Edition / April 2007, recommends Community-based ecotourism in the Rurrenabaque area:
Chalalán Ecolodge http://www.chalalan.com
A Day for the Communities Tours, TES, Turismo Ecológico Social
Mapajo Lodge http://www.mapajo.com
San Miguel del Bala Eco-Lodge & Eco-Tourism http://www.sanmigueldelbala.com

For more information you can follow some of these TT tags:

Bolivia_FAQ (Frequently Asked Questions): http://www.lonelyplanet.com/thorntree/tags/Bolivia_FAQ
Rurrenabaque: http://www.lonelyplanet.com/thorntree/tags/Rurrenabaque
Rurrenabaque_Jungle_Pampas: http://www.lonelyplanet.com/thorntree/tags/Rurrenabaque_Jungle_Pampas
Bolivia_flight: http://www.lonelyplanet.com/thorntree/tags/Bolivia_flight
Bolivia_malaria: http://www.lonelyplanet.com/thorntree/tags/Bolivia_malaria