Our savings accounts are on a quarterly statement cycle (unless there is ACH activity then it cuts monthly). We also currently service charge the account quarterly when the statement cuts if the balance drops below $100. My question is, is there any reason why we couldn't change it so the service charge is charged monthly at the end of the month, but the statement would still cut quarterly?

That's OK, as long as you send out a change in terms to inform your current customers of the change.