I was able to just set up an account with Coinbase, they asked for my name address and bank ACH transfer info.

Is anyone aware of a web based property management system that allows online rental payments with ACH and automatically charges late fees when the rent is paid late?

One of the biggest head aches as they all say is good contractors.

This is a new rental and after some research I decided to try out cozy for online payment, and I was aware of the 5-7 day processing time through ACH.

I would advise direct ach transfer of rent so no one is collecting.

If you keep asking, they'll find something to belly ache about just to make you happy. 

Most property management software solutions are going to include ACH payments and some even have cash payment options where the tenant pays at 711, Walmart, CVS, etc and it electronically deposits into your account.Here's some software options that I commonly see recommended on BiggerPockets.

Remembering that one said that he would collect check or cash in person, and even though the tenant wire/ACH rents, he would still handle over the receipts to them, just to walk thru his properties periodically, not only inspect the properties but also get information about his tenants.

Setup ACH through Chase with a business account.

They begin to trust you with every on-time/early mortgage payment- I always set the ACH a day or 2 early.