Our son had very similar problems... excellent plate skills, but arm/throw issues. We found that he could throw hard from say, third base, but from behind the plate he somehow lost a lot.
We did many different things, read a lot of different things, talked to a lot of different people, went to catcher camps, etc.
First, one of the biggest keys he experimented on was getting his footwork and motion down to the place where he could be comfortable and quick... just getting rid of the ball quickly was a big key. That took a lot of thinking through things, tweaking, observing.... "feeling" the motion and the ball. A good exchange from the glove was important. The caution here is that as many catching experts as there are... there seem to be just as many variations in technique. Hate to put it this way, but we found a lot of "dogmatic experts" along the way. In the end, he had to decide what worked for him (yet keep an open mind). Also, sometimes some techniques work better on the second go around. Anyway, having said all that, I think the best catching instruction we got was from the UVA staff at a clinic they did near us. Another good session was with Al McCormick, who frequents this website. We drove down to MD to see him one time and it was well worth the trip. Of course this website has also been a gold mine of information and support... for which we have been very grateful.
Second, we found some good training materials at
http://www.baseballstrengthtrainingsystems.com/. It's not too glossy, but it's the best stuff we found to date. Son is also on the lookout for various baseball-specific exercises that he incorporates along the way. He trains very hard during his off-seasons... and in-season too. I'd say that a lot of abdominal/core work made a huge difference on his throwing... and the right amount of weight work (dumbbells, bands, "rice buckets", etc.). I actually think this probably had the biggest impact. Even though our son is "big and strong", there were certain things he needed work on... things that turned out to be pretty important. Catching is extremely physical (and mental)... so good physical training is important.
Our son is now in his second season at college (small DIII). He backs up an all-conference catcher, but he now also has a reputation for a strong arm... and now gets more playing time. Last game he completed a fairly rare 1-2-3 double-play that NO ONE thought he had any business trying... but he got the trail runner at 1B with a rifle throw. Even last year, I doubt he would have pulled off that play. He's also finds that he is getting compliments from other teams... and umpires. It's just little stuff, but they are nuggets that help keep him going when things get a little tough. The point here is that we're talking about a kid who did not even try out for baseball as a HS freshman and really did not play until his Junior HS season. So, the training, the techniques and the effort really does work.
This brings up my third and final point... some things just take time. Our son started late. But, it sounds like yours is starting early... and that's great!! As long as he loves the game, don't let him give up. This sport is more like running a marathon than any other sport I have been around (except running a marathon). It requires much more patience and pacing than is evident. <grin>.