It is relatively safe, but do read and heed safety tips about visible valuables, staying off deserted streets even in more upper class areas, carrying lots of money, etc.
However, how comfortable it may be really depends on what kind of traveller you are.
Brazilians are very open and strive to be helpful. Few people speak English, though, so do bring a phrase book and/or dictionary, write things down in Portuguese (place names) and be prepared to mime/gesture with good humor.

Salvador can be done on your own, by local bus or taxi. Priority is the Pelourinho historic district, down the Elevador Lacerda to the Mercado Modelo, by taxi over (and back, do wait for a taxi and do not walk) to Solar de Uniao, and by "Ribeiro" bus from the base of the Elevador (called the Comercio) or by taxi out to the church at Bonfim. You can walk from the church through the neighborhood to the beach in Monte Serat to have a beer with the locals and then get a bus or taxi back. All these places can bee seen on video on YouTube to get an idea of what they're like. A good intro site is www.bahia-online.net

Sao Paulo ideas:
http://travel.nytimes.com/2011/03/13/travel/13hours-saopaulo.html
http://www.nytimes.com/slideshow/2011/03/13/travel/20110313-HOURS.html
http://travel.nytimes.com/2007/10/14/travel/14hours.html

Rio:
A good intro site with lots of info is:
www.ipanema.com
Very easy to get around to the main sights by inexpensive taxi, and some places by metro. Write down where you want to go and have a card from your hotel to show for the way back.

It is absolutely fine to visit without knowing Portuguese. If you know some Spanish that will help. The security issues are overrated and if there are three of you, that is better than if you are on your own.

Security issues may be overrated only until something untowrd happens to you personally. Although it seems conditions are getting better in some locations, there is still a great deal of poverty and it behooves any foreign traveller to remain vigilant at all times.
IMO it is best to be solo, and therefore not calling attention to yourself (as a potential target) by chatting away amongst yourselves in a foreign language.

Six days for three of Brazil's biggest cities which span a range of a couple of thousand miles is at the madder end of the scale of any proposed trip I have ever seen. Seriously, your itinerary will cause you more harm than any street kids ever could.