Whilst we don't yet seem to have a copy of the original sheet music for The Knickerbocker Line, what we do know is that the song had minstrel predecessors that didn't have the ju-be-ju in them. As I stated earlier the most comprehensive study is in Cazden where he devotes 11 pages to the history of the various relatives (pp543-554) including 2 variants from tradition. He looks at British and Australian adaptations. Although the Knickerbocker Line is obviously from New York a Glasgow broadside of 1876 has a completely Anglicised version that mentions Bristol and London.

If it helps there appear to be 2 variants of the first 2 lines of the chorus, the one we are dealing with here that rhymes ju-be-ju with through, and the other runs something like
Watch her, twig her, watch her how she goes,
Her high-heeled boots and patent leather, my Ginny she's on the go.
(Knickerbocker Line)

Those of the family that have ju-be-ju are.

Cruise of the Bigler (after 1866) Rickaby version
'Watch her, catch her, jump on her juber-ju'

Dogger Bank (Sam Larner, Norfolk, England)
'Watch us, twig us, we're a popular juby-ju'

Erie canal Song, Lomax
'Hit 'er, shove 'er, go up in the juber-ju'

Ten-thousand Miles From Home, Lomax
'Watch her and catch er, and jump her juberju'

Ives, learned in a Boston Lumber Yard
'Oh watch, catch her, chiv up her jubeeju'

Doerflinger.
'It's watch her, it's catch her, she's up in the ju-be-ju'

Sandberg.
'Watch her, catch her! Jump up in her jujubaju'

Whilst I like the 'doux bijou' explanation, most of these seem to be referring to something aloft on a sailing ship.

I think the 'juba' link is a red herring.