I've been to Plitvice twice - once in early October, once (recently) in mid-May. Both times, I started at the upper lakes (south, closer to entrance #2), which in my opinion offers the slightly better waterfalls (not that the lower lakes falls are so bad). As I recall, the best time to shoot most of the waterfalls is in the morning. By afternoon, you aren't quite shooting into the sun but almost. Depends in which falls, of course, but many of them seem best photographed in the morning.
I have been out first thing in the morning both visits and that's what I recommend. Get there at 7am when the park opens the second day you are there. If you are at Entrance #2, you can take a short boat ride across to the start of the upper lakes trails, but the first bot from the upper to lower lakes (from the boat launch near Entrance #2) may not start running until late - 8am? If you get out there that early, you'll still be able to use your tripod for a while; once the boardwalks are busy with tourists later in the morning, it's hard to keep your tripod steady as they walk, not to mention it can be hard to keep them out of your shots. In some areas you can set a tripod down on the ground but sometimes you have to set it on the boards, because there's a drop-off to the water below.