Since Lat Krabang is a khet in Bangkok I don't think it's possible to visit Samut Prakan Immigration even if it's more close than Muang Thong Thani. But if they ask Samut Prakan it would be nice to know. I live in khet Nongchok which is neighbouring Lat Krabang and also very far from Muang Thong Thani.
I had problem several times with 90 day online reporting so I started to use the old fashioned Thailand Post mail service. It works perfectly. I send the required documents with registered mail. I enclose a pre stamped empty envelope for the receipt. I get my receipt in return in about 5 days.