I can understand why people would put Shiraishi above Fuji. Ultimately... it comes down to who has the better record. And Shiraishi is 1 win and 0 losses when fighting Fuji.
Saying that Fuji lost to Shiraishi because Konomi didn't want to Fuji to win is pointless. Fuji beat Kirihara because Konomi wanted Fuji to win. This is the same with all of the matches in PoT. Konomi decides who wins and loses.
It's difficult to ascertain the exact numbered ranking as there are a number of matchups that have not happened and probably never will. Using a tier system is a lot easier then an exact ranking.
1st tier: Echizen.
2nd tier: Yukimura (predicted), Tezuka, Kentarou (predicted), Chitose, Atobe
3rd tier: Sanada, Shiraishi, Fuji
4th tier: Kirihara, Tachibana, Oshitari (bit of a stretch, but I'll put him here)