I have a suspicion that despite what John's marriage cert says, this is him on the 1881 census. part of my reasoning for this is that I can see that on the same ship as John, also sent by Leeds guardians is a Thomas J Crowther aged 8.
Helena Crowther 26 - married, b Wakefiled
John R. Crowther 3 - b Scarborough[ the image does look like R rather than P]
Thomas J. Crowther 1 - b Wakefield
Address 25 Woodhouse Cliff, Leeds
Ref: RG11, 4530, 87, 27
Helena can be found on 1891 and 1901 - still claiming to be married, but not with a husband or children
This would be the marriage - she's with a Widdop sister in law in 1891, so this would make the father's name correct.
Oct - Dec 1873 Leeds Vol 9b, p779
Samuel Crowther <<<
Eliza Lang
Isaac Pickles
Helena Widdop <<<