It depends what you mean by “better”, I suppose. I will answer in terms of combat effectiveness though.
As a general rule, I would say Muay Thai is better for combat. Similarly to Kickboxing, Muay Thai has effective punching and kicking techniques that enable you to punch and kick well as well as counter those attacks well. However, Muay Thai also provides you with additional ways to attack which Kickboxing (American) doesn’t, for example, Muay Thai teaches clinch fighting and the use of elbows and knees as well as backfists. Kickboxing may be a tad better in terms of punching training but Muay Thai more than makes up for this through adding in elbows and knees.
Conversely, though, some styles of Kickboxing are just as effective as Muay Thai. For example, Dutch Kickboxing which is based more on Muay Thai is pretty much equal to Muay Thai as it has the elbows and knees too, plus it uses mostly Muay Thai kicks rather than Karate kicks. American Kickboxing derives most of its kicking techniques from Karate. Therefore, arguably its kicking techniques are less effective than Muay Thai because in Karate kicks are delivered via the instep rather than the shin. The benefit of the Karate kick is increased speed and range, whereas the benefit of the Muay Thai kicks is power and durability as the shin is much harder than the metarsals which means they cause more damage and are less likely to be injured. Furthermore leg kicks are not usually performed in American Kickboxing.
In conclusion, Muay Thai is more effective than Kickboxing in my opinion as the main style of Kickboxing which is American Kickboxing does not include elbows, knees, backfists and leg kicks. Furthermore, the Karate kicks which American Kickboxing uses aren’t as effective as the Muay Thai kicks are. It is important to remember though that Kickboxing is not a monolithic martial art, there are different styles of it which vary greatly and some styles such as Dutch Kickboxing and K1 Kickboxing are equal to Muay Thai in terms of effectiveness.