Online virus scanning service with remote file submission?
There are services like ScanThis! and URLVoid which are similar to VirusTotal. None seem to have an API that you are looking for. However, more interesting is how effective these systems actually are. Passing the EICAR test virus pattern to ScanThis! for example, comes back with a "not infected" report. URLVoid, however, does indicate the file is infected.
In addition to finding an API, you will also want to ensure that the service you select has an appropriate scanning engine. If you have samples of infected files, then it might behoove you test them to ensure that they are effective. Otherwise you're no better off.
I tried NoVirusThanks.org and it worked fine. There isn't an "API", but you can alter the generic submission link so you pass the parameter (ie remote file link) you want to be scanned, essentially manipulating the GET method of the program (nothing malicious though).