There is not such a scanner as the best free URL scanner. There is a series of scanners that can be combined to get more reliable and fuller results.
For IDS alerts you use another scanner as for website malware, iFrame malware and PHP malware, bot malware etc.
So use several scanners like Zscaler Zulu, Quttera's, sucuri's, evuln, urlquery.net on a suspicious link.
wepawet, blacklist scanners, DrWeb's url checker, WOT, saferpage.de, urlvoid and ipvoid, virustoital, clean mx,.
Also google the domain name and the IP the suspicious URL is on. There are also special scanners just for the security aware, that should be used with script blocking active and in a virtual machine/sandbox, like jsunpack, redleg's file viewer.
We have a specific group of users in the virus and worms section that have developed quite some expertise in this field - !Donovan, Pondus, mchain, and several others that know about website analysis and malcode. Go through several of their posts to see what this all means,
polonus
