I have to do a visa run, to get a tourist visa, to then convert that to a Non-Immigrant B/work visa once I'm back in Thailand.

I was refused a tourist visa in Cambodia before COVID. I believe it's in the embassy system, so it's likely better to get the SETV from another embassy/country. However, the reports and suggestions about visa runs are basically all to go to Cambodia, which isn't an option for me.

 

Excluding Cambodia, what is the best option for a visa run?

Any reports about the other countries (Singapore, Malaysia, Indonesia, Vietnam)?

Pre-Covid, Singapore was the goto place for a nice few days coming back with 2-3  Month Tourist Visa. 
Check if Thai Embassy there doing that plus entry requirements.
 

Also heard Malaysia (Penang) might be good with agents possibly re-starting visa run packages. 

With regards to current travel requirements and historical "friendliness" of the Thai consulate in HCMC and Thai embassy in Hanoi, Vietnam looks like a good  nearby option. But I haven't seen any recent reports (they reopened the country to tourists less than a month ago).

While it would not be cheapest, the best nearby consulate for tourist visas (when you have bad stamps in your passport) immediately pre Covid-19 was Yangon. Unless you assess the risk as high, you do not need to use Myanmar, however. If you are just worried about history at one specific embassy (and have a new passport since) any embassy/consulate should be fine, though avoiding Phnom Penh would be prudent.