Should the retirement plan box be checked on a W2 even if I have been retired from the company more than 3 years and exercised stock options in retirement?

No.

Stock options are not a retirement plan. And you should not have box 13 checked for retirement plan for exercise of your stock options.

See chart on page 31 of this IRS document.

You may want to reach out to your previous employer for a correction if this hinders your ability to contribute to an IRA or Roth IRA.

Thanks! I also receive a company pension. Would that trigger the box to be checked?

No. 

Per IRS: Employer should check the retirement plan box if an employee was an "active participant" for any part of the year in:

• a qualified pension, profit-sharing, or stock-bonus plan under Internal Revenue Code Section 401(a) (including a 401(k) plan).
• an annuity plan under IRC Section 403(a).
• an annuity contract or custodial account under IRC Section 403(b).
• a simplified employee pension (SEP) under IRC Section 408(k).
• a SIMPLE retirement account under IRC Section 408(p).
• a trust described in IRC Section 501(c)(18).
• a plan for federal, state, or local government employees or by an agency or instrumentality thereof (other than a 457(b) plan).

Some additional information. I receive a qualified pension  but I am no longer an employee. Trying to understand if I am considered an active participant in the plan even though I'm no longer an employee. The definition of active participant seems to indicate being an active employee which is not the case.

According to this excerpt from an article on the subject by the IRS, it would depend on the type of plan, but in general you would only be a participant in an employer retirement plan if you made or could have made contributions: