Online scanners are checking files already located on your computer (in memory or on the hard drive) so it does not matter which browser you use. What the online scanner does NOT do is install anything into your browser to watch for future attempts by malicious websites.
An active virus scanner should always be running in memory on your computer to watch for files from the web or inserted USB thumb drives, etc. And the better products also incorporate add-ons into your various browsers to detect dangerous scripts from running. Online scanners do not do these things and should never be your only anti-virus solution.
Also, many nasty sites offer so-called free online virus scans but are actually installing malicious programs that are in fact themselves a virus, giving you popups saying you are infected and to buy their software to have it removed etc. So be sure you use a reputable online scanner. We have several listed in our
Freeware DB.