It's kind of tough to get from Puerto Maldonado To La Paz. There might be a very complicated way to do it from Puerto Maldonado, such as via the Heath River Wildlife center which is actually in Bolivia, but I am not sure if there's an official border around there or if you can get to anywhere else in Bolivia from there. I doubt it.
Another option is to take the bus from Puerto Maldonado to Puno. This is not a common route and I don't know much about it, other than it takes about 10 hours. You could then cross the border from Puno via Yunguyo/Copacabana (taking in the Lake on the way) and then continue on to La Paz. However, the little I do know about the Puerto Maldonado - Puno route involves a bus hijacking in September last year. I have no idea how common that is and I really don't want to scare-monger (I think most of the routes have been subject to occassional hijackings), but I can't blindly recommend doing this, as the only 'experience' I have of the route is meeting people who were on that bus.
I think that most people would recommend flying from Puerto Maldonado to Cusco and then on to La Paz by plane or bus (if you want to visit Lake Titicaca on the way).
Is there any particular reason you want Puerto Maldonado to be at the end of your Peru experience? it might make more logsitical sense to switch the itienrary around and go: Lima-Puerto Maldonado-Cusco-Puno-La Paz. Just a thought.
I found a few previous threads on a similar subject:
on this subject:
My husband and I are looking at this same option for October. Does anybody have any updates on this route or is still not advised?
Thanks for any comments.