And if you have both programs on your machine you can run MLwiN from 'within' R
http://www.bristol.ac.uk/cmm/software/r2mlwin/
Zhengzheng Zhang, Richard M. A. Parker, Christopher M. J. Charlton, George Leckie, William J. Browne (2016). R2MLwiN: A Package to Run MLwiN from within R. Journal of Statistical Software, 72(10), 1-43.
Just to say that MLwiN can estimate these models with likelihood, MCMC and iterative bootstrap procedures - and it is comparatively very fast as software reviews have shown.
xxM, an R package developed by Paras D. Mehta, can handle unlimited levels and more complex cross-classifications. Please check https://xxm.times.uh.edu/ for more detailed information. Hope that helps.