Andrew Whitehouse said:
Campos do Jordao sounds interesting, although I'm a bit worried it might be either fully booked up or expensive, as from what I've read July is the peak season there. Will look into this a bit more. Apart from the section on Arthur's site, there actually doesn't seem to be much information on birding there.
I'm also wondering if anybody would recommend Parati as a base for the lowland forest rather than Ubatuba. Parati sounds like a pleasant and easy place to stay and Arthur's site mentions some good birding in the fairly near vicinity. Anyone know anything more?
It seems Brad & Dalcio have answered most, but just a few additional notes:
Parati is a nice town, although perhaps a bit touristy. As for birding, however, I'm not aware of any good localities near the town, although there's one or two trails that run through some secondary forest/shrub near town that perhaps could reveal something interesting (the most interesting thing I've had when walking these trails, mostly to get to nearby beaches, is Brazilian Tanager. It's nice, but easy many other places). There are far less busses going through Parati than through e.g. Ubatuba (which also is closer to the main localities), but the busses that run up and down the coast via Parati may still be able to get you somewhat near one of the birding localities (but the localities I know in this region would still require perhaps 15-20 km. walk from the nearest place where a bus can let you off and for this reason perhaps can perhaps not be recommended without access to a car).
Horto Florestal near Campos do Jordão is very easy. There are hourly busses that do the short tour to the entrance of the park (beware that this park is very popular among locals, especially on Sundays. You may want to avoid Sundays, esp. if during a local holiday, as it may be rather crowded then). The bus to the park run along the main road in Campos do Jordão, so you don't even have to walk to the bustation for that (just ask one of the locals which side of the road you should stand on - to get the bus in the right direction). There are a few trails in the park and they all seem slightly different, so doing all may be a good idea. The Araucaria Tit-Spinetail is common throughout the park (I've even had one taking a sh... on my forehead!), but a bit of a pain to watch as they usually stay in the top of the distinctive Araucarias. The trails going to the left shortly after you enter the park are, in my experiance at least, the ones that are best for Hellmayr's Pipit and nightbirds (but there's also a road before entering the park that's good for nightbirds - mentioned on Arthur Grosset's page). The trail towards the waterfall is, in my experiance, the best for Black-capped Piprites & Cotingas (Swallow-tailed Cotinga & Red-ruffed Fruitcrow; both probably seasonal and unlikely to be seen during Austral fall/winter). The Warbling-finch commonly seen in flocks is the nominate race of the Red-rumped. It often seem to cause confusion (indeed, when I saw it the first time a number of years ago, it confused me too) as it looks so utterly different than the widespread southern race cabanisi which is the one shown in most books. White-bellied Warblers & Sharp-tailed Streacreepers seem to hang out at most smaller streams throughout the park (but latter is surprisingly easy in several localities in SE Brazil - at least for anyone familiar with the MUCH harder Andean populations). Also, if visiting during the South Hemisphere winter (= North Hemisphere Summer) do bring a jacket (if I'm not mistaken the coldest temperature ever measured in Brazil was in Campos do Jordão). There are other localities near Campos do Jordão that have some nice birding (e.g. the road to Pedra do Baú mentioned on Arthur Grosset's site), but I'm not really sure they can be done by public transportation (perhaps it is possible, I've just never tried). Also, if doing both Campos do Jordão and Itatiaia it might be worth mentioning that these two are easily visited via Resende. As far as I know there is no good birding near Resende, but it's a transport-hub with bus-connections to both Campos do Jordão and Itatiaia (a few a day to Campos do Jordão, one every hour or so to Itatiaia). So, you don't have to waste time going all the way back to Rio or São Paulo to connect Campos do Jordão & Itatitia.
By the way: As said - don't even think about safety on the busstations. City busstations are usually filled with people and guards, so they're probably safer (at least when discounting pickpockets) than most other places where tourists happily walk around in Brazil. Brazil has a bad reputation and there certainly are many places where the risk of being a victim of crime is high, but if using common sense and staying away from such "bad" locations (most of which are wellknown and easily avoided by reading safety advice in handbooks and/or asking locals) you're likely to stay clear of trouble.