I have a 4 year old Japanese Larch and would like to prune the leader as it grew very quickly last year and has very few branches compared to the bottom half of the tree which is nice and bushy. I would also like to control the size of the tree (sort of like an 8 foot bonsai). Will I damage the tree?
You will have to prune more than just the apex if you want to maintain your larch at this size. It isn't a great deal of work, amounting to a few hours two times each year. Since you are wanting a landscape planting to remain about 8 feet tall, you will need either a pole mounted tree pruner or (better) a 3 legged gardener's ladder and a hand pruner.
You want to do structural pruning in late winter (i.e., buds are about to are are beginning to swell, but haven't cracked showing green - even then is okay, but no later). Cut back to a bud. The most distal (farthest from the roots) will usually become the apical meristem for that branch. If there should happen to be too many buds too close together somewhere, just pick off some until the concentration of buds is about like elsewhere. Shorten all branches near the top so that only one bud on one stem is the highest from the ground - this will be the leader.
In spring prune off part to most of the new growth at the branch ends when the new shoots have extended and their color has has darkened. This will cause branching back inside the canopy which must have in order to keep the tree at whatever size you want. These interior branches must get some light, so you may need to do some thinning of the foliage so that light gets to the interior.
You likely could start within the next few weeks or so, doing your first structural pruning. Shorten the leader and branches, remove branches heading back toward the trunk, etc. Anywhere there are more than three branches emerging from a point, reduce it to only two (this prevents knobs from forming). Generally a branch will die if you remove all the buds on it - always leave a bud if you want the branch. Then (probably about May), cut back the new growth and enjoy your tree. Next year about this time, you'll again do structural pruning, shortening branches (back toward those new ones you made with the late spring pruning), fixing mistakes, etc.; pruning harder in those areas where growth has been more vigorous than in less vigorous areas (restore 'balance').
Because the tree in question has the genetic potential to grow far taller than 8', and so in keeping it at that low height, you will essentially be pollarding the tree. You may not really like the result. It's normal for trees to grow tall and lanky before filling out. Usually, if people want them to look full and bushy as they grow, it is done by heading back (taking the last season's growth back, but not entirely removing it). This causes more branching, but also maintains proper proportions regarding to apical dominance, so you can maintain a healthy leader. If you cut the whole leader off, the plant's response the next season will be to put out a whole club of new leaders, which is not natural looking, or in the long run, structurally sound.
So I would recommend heading back as possibly the heaviest pruning you should do, taking back up to 3/4 of all the new growth (if it is very long/whiplike), and then do similarly as the tree grows and matures. Just remember, the further you cut back, the more long shoots the cut end will throw out. For an '8 foot bonsai' look, I'd choose a tree with a maturing height in the 8' range.