I have been in Thailand almost 2 months. I have a US passport and received 30 days on arrival. After the first 30 days, I paid to extended 30 more days at the Thai Immigration Bureau in Bangkok (i don't think i can pay again for 30 days). Now I'm in Krabi and would like to stay 30 more days. Would it be a good idea to do a border run to Malaysia? I am not sure what the process is for US passport. Or would it be easier to go by plane for example to Singapore, stay a day or two then fly back to Thailand and get 30 more days on arrival in the airport?

You could do it at a land border crossing without a problem. Dependent upon the crossing to Malaysia you use you may be told you need to stay overnight.

You could also do the crossing at Ranong to Myanmar which may be closer than Malaysia.

Jump the plane to Penang for the day (or 2). Worth a look anyway

Go over to Langkawi for a couple of days, the Skybridge there is something else. You can get a taxi from the border at Padang Besar to the ferry at Kuala Perlis for about 500 baht and is just under an hour. If going best to look at the Cenang beach area.

You need to stay 48 hours if you want to benefit from the duty free.