All non-profits, regardless of income, must file the appropriate 990 Form with the IRS annually as well as any state forms required. Failure to do so for three consecutive years will result in the IRS automatically revoking your federal tax exempt status.
Leagues under the Little League group exemption number should use a 10/1-9/30 fiscal year putting their filing deadline at 2/15.
The league must also submit an annual financial statement to Little League Baseball, Incorporated. A sample financial statement is available at LittleLeague.org/FinancialStatement.