Michael’s marriage to Ellen was registered in Magherafelt Oct – Dec 1896 Volume 1, page 1081. If you get a copy of that certificate it should give you his father’s name.
However it looks as though it was also Michael. Here’s the abstract (summary) of his will, which mentions sons Michael & Charles and daughters Kate & Mary. No mention of any wife so she will have pre-deceased him. No mention of John or Arthur.
Full Abstract : The Will of Michael M'Crystal late of Anagh County Londonderry Farmer deceased who died 3 September 1875 at same place was proved at Londonderry by the oaths of James M'Crum and James Sheils both of Anagh (Desertmartin) Farmers the Executors. Effects under £100
The full will is on the PRONI website.
There’s a probate file for Michael junior too but it has not been put on line yet. He died intestate so there won’t be a will but there will be a file with some details of his estate. You would need to get a copy from PRONI in Belfast. Here’s the abstract:
Full Abstract : Administration of the Estate of Michael McCrystal late of Annagh County Londonderry Farmer who died 14 February 1908 granted at Londonderry to Isabella McCrystal the Widow. Effects £207
Griffiths shows Michael M’Crystal on plot 21 in Annagh & Moneysterling in 1859 (a farmhouse and 10 acres). I’d therefore guess that Michael junior was born there, and I’d search the local parish records for his baptism. (Statutory birth registration didn’t start till 1864). The 1901 census says he was born in Co Derry so I would go for the most likely source first. (Parish of Desrtmartin). You'll likely find his siblings there too.
(The 1831 census for Annagh has a Michael and a Thomas McCrystal there, each with a separate household, so it looks as though the family had a fairly lengthy connection with the area. You would wonder therefore how 2 children came to be born in Cavan and Fermanagh, and why they aren’t mentioned in the will. Farmers didn’t move about much. Are you sure you have the right families?).