What type of visa should I apply for if I plan to stay in Thailand for 90 days with a 60-day initial stay?

For your stay in Thailand, you should apply for a single-entry tourist visa (TR), which will initially grant you a 60-day stay upon entry. As you approach the end of this period, you can apply for a 30-day extension at the local immigration office. If your wife is Thai or you are over 50 years old, you may be eligible for a NON-O visa, but the tourist visa is recommended for your situation.