I've messed with most of them, except the Jr. Out of the last 3 2600s I ran into, the only one that was fully working was a worn 4 switch woody that was badly beaten up. the case had chips and cracks all over it, so I pulled the board out of it (revision 12) and stuck it into a Vader shell that had a bad board. So I have a nice new looking Vader, that I did the LED and AV mods on. So, in my recent experience, I'd lean toward looking for one of the 4 switch woodys. Of course any working 4 switcher would be fine. As far as the 7800 goes, mine works great, but the plastic on them is very brittle, so you have to be careful with them. I AV modded mine and I use it quite often, even for my 2600 games. The cartridge connector on the 7800 is too tight for some games, but if you ever have the system apart, to do an AV mod or something, you can remove the plastic part of the connector and file out the corners and reinstall it. Then all the carts will fit. I don't have any experience with the Jr. but I have been tempted to buy one, just because it's smaller, making it more carry friendly if I want to take it with me somewhere.
If you buy an Atari off eBay, just makes sure the seller has plenty of positive feedback and lists the console as "Tested and working". Good luck on getting your Atari!