I know I found the option to do this in Windows but I couldn’t find it in my Linux Mint version of Thunderbird. The default behavior seems to be starting your reply at the bottom of the last message you received which is actually considered good etiquette for mailing lists and such but when responding to personal emails I like to reply on the top.
For some reason I couldn’t find this in the normal settings so I went to advanced under Edit -> Preferences -> Advanced. Under the General tab, click on Config Editor then type “reply” into the filter box. The entry you want is mail.identity.default.reply_on_top which was set to “0”. Set it to “1” (true in boolean) and you’re set!