To the OP, Toon Link practically baits Ness. If you're going to use bombs, use your boomerang or arrows first. Throwing the boomerang at a diagonal angle makes it tougher for Ness to get close, because it creates a double layered wall making that V shape. Toon Link is a lot quicker than Ness as well. I think your problem is is that the Ness' you're fighting either know the match up better or you're using a certain method that they've adapted to, which is no longer working. I fought a Link that was playing spammy and campy as Toon Link, which I don't think is a good option for Link. He was creating a wall of projectile, applying pressure that way and forcing me to approach. He even jumped and fired arrows, making it that much more difficult for me to get close. The first two matches were close, but the third match I had with him, I had figured him out and used the lag behind his projectile game as my advantage to deal damage on him. That was the match I did the best on. So again, the Ness' you're fighting either know the match up, or are adapting to your play style. I'd imagine that's what's happening to you.
I've noticed that all but one aerial attack have the least amount of lag for Toon Link, and that's his neutral air. Toon Link's back air is a good kill move, no doubt. If you catch Ness off stage, you can go for a back air, even a forward air, and kill him. You can try to disrupt his PK Thunder with your arrows if he's not recovering low enough. If he is recovering below the stage level, you may want to go for a bomb, though that might bring him back up. Even then, doing so may allow you to throw in a smash attack. If Ness is approaching you from the air, you can shield grab him and punish him that way. I'm sure you'll figure it out eventually. I can't stand fighting Toon Link because of his projectile and speed, and I still have trouble against him.