My knowledge of the divisions of London is rather vague. If a church is wrongly listed here, please let me know!

Whitechapel on Wikipedia.
 

East London Mosque (aka Council of Mosques) on Whitechapel Road.  Interior view. TQ 344 816. © Mehmood Naqshbandi, and reproduced from his website Muslims in Britain.

Church of the English Martyrs (R.C.) on Prescot Street. TQ 3389 8091. © Chris Kippin (2021). Link. Grade II listed, wherein it's dated to 1875, by E.W. Pugin.

Free Presbyterian Church of Scotland on Varden Street. I can read "Zoar Chapel" in the stone above the windows.  TQ 346 814. © Chris Kippin (2021). The church website advises that the church was bought in 1974, and was previously owned by Gospel Standard Strict Baptists. Although it looks to be of Victorian age, it isn't labelled as a church on O.S. maps of 1898, 1916, or 1960. The website also mention previous meeting places, including Eccleston Hall (of which there is a photo) - where was this?

Ishaatul Islam Mosque on Ford Square and Damien Street. TQ 351 815. © Mehmood Naqshbandi, and reproduced from his website Muslims in Britain.

Markazi Masjid (aka Maarkazi Mosque), on Christian Street. TQ 345 812. © Mehmood Naqshbandi, and reproduced from his website Muslims in Britain. 

St. Boniface German Roman Catholic Church on Adler Street. TQ 3420 8144. © Chris Kippin (2021). Link1. Link2. Numerous interior photos here. Its grade II listing advises that it was built in 1959-60, preceded on the same site by an earlier St. Boniface of 1875, destroyed by bombing in 1940 (an interior photo of this church is available here). In turn, this was preceded by Zion chapel, which collapsed in 1873.

St. George’s German Lutheran Church on Alie Street. Its grade II* listing dates it to 1762-3. TQ 3398 8123. © Chris Kippin (2021). Link.

The former St. Paul (1847-1990) on Dock Street, now a nursery. TQ 3417 8079. © Chris Kippin (2021). A good history here. The very brief grade II listing.

Whitechapel Mission stands on Whitechapel Road and Maples Place. Working for the homeless, it's unclear from their website whether services take place here, but it is a Methodist organisation, and the building stands on the site of Brunswick Hall, a Primitive Methodist Chapel. This source dates the present building to 1969-72, and the earlier chapel to 1866, which it says had been built as Calvinistic Methodist, and later Congregational before the P.M.'s took it over. TQ 3486 8183. Link.