Googling this question produced good answers, but I'll sum them up here anways.
First and foremost, the use of many agents is not abnormal. From former agent James Gagliono
"In the FBI, we tend to defuse situations by removing the fight-or-flight inclination, via our overwhelming presence. To arrest one, we bring 10. For 10, we'll bring 100," (source)
Especially for such a polarizing figure where, if somehow people knew the arrest was going to happen, there would likely be both protesters and counter-protesters:
"They have the responsibility to not only protect their agents, but the public at large and even the person they are arresting. Often the way to do that is with overwhelming force that would tend to dissuade any resistance." (same source as above)
Stone likely exacerbated fear by posing for pictures armed at a gun range joking about "shooting "commie dogs" and making a "JFK throat shot,"" and saying that if Trump is impeached that "there will be a civil war in this country."(source)
Now Stone is a well known provocateur, and to those who know him it is clear he's just making noise to get people riled up, but the FBI can't justify seeing a man making threats about shooting Americans and predicting a civil war and just say "eh, he's probably joking".