Correction
1. How to I say"sorry for my late reply" in Japanese? ※ How to I say→ How do I say
2. 本当にありがとうございます。→よろしくおねがいします。I hope you will take care of me.=Thanking you in advance. To say ありがとう is strange because you haven't known whether someone gives you a favor. It might be a correct expression in English. But in Japanese, we don't say "ありがとうThank you" before we know someone gives us a favor.
Answer
"返事が遅れてしまい、申し訳ありません" is correct when you reply after passing the time limit for answering. "返事が遅くなり、申し訳ありません" is used when you reply late.