There are several ways to lower your bike, from cheap to expensive. All have their advantages and issues. Warning: When you lower the bike, your frame and foot pegs go down. Do only as much as you have to, you will bash your skid plate and kick bad stuff that others will clear.
The cheapest thing you can do is cut your seat foam. You can do this yourself, it's pretty easy, but you’ll need a very powerful stapler to put your cover back on. Take out 1" to 1 1/2" and you'll really feel the difference, in height and comfort There are many companies that sell a lower seat pad with a wider profile and more comfortable foam, I’ve used Seat Concepts and like it much more than when I just cut down my stock foam. You’ll notice immediately that when sitting you've just raised your bars and tightened up your knee bend. Some people don't like that, while others feel better balanced sitting lower into the bike.
Also reasonably cheap and easy is a lowering link. I've used a Kouba Link on a couple of my bikes, there are several other manufacturers of lowering links out there. They’re very easy to install and don’t cost too much for most bikes. Usually several different lengths are available, but the more you drop the seat the more it affects your suspension travel. You’re changing the length of a lever arm in the middle of a very complex mechanical system. Here’s a quote from the Kouba site FAQ’s: “They put more leverage on the rear spring and make the rear more compliant on the small stuff but may require a heavier rear spring to help prevent bottoming if a rider is very aggressive.” In my experience the model that drops your seat about 1" is the best compromise, going more than that and the suspension tuning and steering problems can start to arise. If you’re not a real aggressive rider, lowering links are great. If you ride “race pace” then you might need to buy a stiffer rear spring. A new spring makes this mod a lot more expensive.
You can take your suspension to a specialist shop and they will put spacers inside your forks and shock. These will restrict the overall length of your shocks, lowering your whole bike by reducing the amount of travel you have available. This service will require new fork springs, and can include custom tuning the suspension valving for how you ride. Cost runs from $500 to $800, and you lose some travel, but if you’re a trail rider with a harsh MX suspension, this mod can take care of both issues. I have lowered the suspension on 3 of my bikes over the years and never liked the ride as much as stock. I cut them down from 1” to 1 1/2” and used 3 different Well Known companies. Many riders post that they Love this mod, posting “Best Money I Spent On My Bike!”
A different rear tire can lower your seat a lot. The typical 110/100x18 knobbie is a tall tire, racing has proven the need for that tall sidewall design. If you don’t race, a Dunlop D606 is a much lower profile dual sport tire, 120/90x18, that is still very aggressive in the dirt and DOT legal also.
Some riders choose to cut their sub-frame. You cut out a small (+/-1/4”) piece of the diagonal strut of the sub-frame and weld it back together. Be Careful- too much and you will bottom your tire into your fender before you use full travel. The subframe and seat will now slope backwards a little; a friend did this to his KTM and it felt weird to me. The back of the seat got lower, the front not so much.
Lower the bike too much and your kick stand will be too long.
If you ride aggressively off road, lowering the suspension a lot can come at quite a cost in ride quality. And speaking from personal experience- I’ve had my feet swept off the pegs by rocks and in deep ruts that everyone else cleared on their taller bikes. And that shit hurts.