Should I apply for a marriage visa or a retirement visa for Thailand from Japan?

The main differences for the initial Non-O and then the subsequent extension is that the retirement route requires less documentation bur the financial requirement is higher. Retirement is often the preferred choice foor this reason and also your Visa status is entirely based on you being over 50 and not still being in a legal marriage.

if you have a long term visa/extension to stay IN Japan as a foreigner you can indeed use the consulate there to get the initial 90 day Non-O (either based on marriage to a thai or being over 50)

Realize once you get here on that 90 day visa you'd need to get a bank account open and get either 400K baht for marriage or 800K baht for retirement banked asap so you can let it season the 2 months required to apply for the year extension at your immigration office for 1900baht

READ the requirements carefully on the website of the consulate you're going to apply at..