A quick go on ebay.com reveals 2-3 suppliers of Smart ForTwo engines, couldn't see any diesels though and at least $1.2K
This site has some ads for Smart Diesel engines starting at $1.4K - rebuilt obviously.
Used Smart Engines > Smart Gas/Diesel Engines & Motors (Buy Cheap)
A quick read of Smart USA/Canada forums suggests that Diesel Smarts are about as plentiful as rocking horse droppings in the US.
There is an Audi A2 1.4 TDI (3cyl) on ebay.co.uk for £950.
Audi A2 1.4 TDI Engine AMF Code Motor Moteur 6 Months Warranty | eBay
A search for Kubota diesel engines on ebay.com reveals a few from under $900. There have been Metro diesel conversions using these, including this one :
From reading up on them though (and this may be incorrect) the issue with them is the gearing which is too low so the engine "pushes against the governor" at cruising speed.
What transmission are you planning on, or will that depend on the motor ?