Is it best to pull credit reports one by one from each agency. Or go to someone like myfico and pull all three with scores.
As Enigma stated, it's best to get all three from each reporting agency inasmuch as it will contain all the applicable data fields. Tri-merges do not have dates of last activity, major first delinquency and applicable account histories.
The individual my fico reports used to be good, but now even they are eliminating some of the data fields. Directly from each bureau is best for disputing, but the scores are bogus - you'll have to go to my fico to get true FICO scores.