Wish is specifically designed for you to be able to cast lower-level spells without the material components
The description of the Wish spell, on PHB 288 makes this clear:
The basic use of this spell is to duplicate any other spell of 8th level or lower. You don't need to meet any requirements in that spell including costly components.
All three spells you cite are 8th level or lower, so you're good to go.
As the components are not consumed by the spell, but rather used for their duration, some more specific explanation is useful.
Spell component specifics
For Leomund's Secret Chest and Magic Jar, this seems unproblematic, you get the exquisite chest and ornamental container - they are 'costly components'. For Clone you certainly get the diamond and the container, though there is the question of whether you get the 1 inch cube of the flesh of the person being cloned. According to RAW, you do ('any requirements'), but your DM might rule the beneficiary actually has to provide his or her flesh.