Right now I'm voting long toss!
There is absolutley no scientific basis for believing long toss programs are a factor in increasing velocity. The only real study done so far, in fact, came to the conclusion that long toss, at best, has no effect and, at worst, can be harmful.
http://www.ncbi.nlm.nih.gov/pubmed/21212502
Add on: If you're going to take the time to make extra throws that put stress loads on the arm, why wouldn't you do it from the mound with weighted balls? I've always found it amazing that those who shout to the skys that excessive pitches are such a problem seem to think having a kid throw 250' a couple of dozen times is perfectly harmless.
I think a good long toss program is a slow steady and consistent program where 250-320 ft happens at older ages and over the course of months of conditioning.
I know my son as done long toss since age 13 over a few months to get ready for the baseball season and has had no ill affects.
There were times when he may have been 50 yds apart and started to feel discomfort and we shut it down. If nothing else it taught him to never throw through discomfort.
I also think part of the success is psychological because when a player is throwing goal line to goal line on a football field there is a certain morale boost. I've literally to the point where I don't feel comfortable catching my son once he draws back in and is at 60 feet away throwing with the same intensity as he was at 300 feet.
A good long toss program is not just throwing but stretching beforehand and relax throws building up to max distance.
I also believe you can make a comparison between distance thrown at long toss to MPH measured at 60 ft.
On the flip side Nolan Ryans "long toss" was no more than 200 ft distance.