I need some help converting this PrC as the Paladin has undergone quite a revision since the book came out.
For starters I'm thinking that any retained Paladin abilities should just become Anti-Paladin ones, including getting Smite Good, and your Divine Bond being limited to the weapon properties of Fiendish Boon, though you still would loose your special mount if you chose that, as you gain the Skeletal Mount.
Bonecraft Armor(and it's improved version and Weapon both seem OK, but I'm not too sure.
Other than that, I think the PrC is more or less fine for PF.
What's this? An Eberron Prestige Class question? Oh-ho!
The take on what the Bone Knight should be converted as depends a lot on your perceptions of both alignment and the country of Karrnath itself. The approach I have taken is that becoming a Bone Knight turns you into a paladin *of Karrnath* not of a particular deity. Sort of like a more specific version of super-cop these are the knight-commanders that would field the undead soldiers of the country in honorable combat during the Last War. I have my Pathfinder Beta conversion in front of me but alas not the actual eberron book to compare the original at the moment. However I do not recall seeing a voluntary or involuntary alignment change from Lawful Good for becoming a Bone Knight, though since Eberron attempts to emphasize more shades of grey in the context of people and their actions simply changing the alignment restriction to "Lawful" could enable a good villainous evil undead controlling knight and your normal paladin under a different color scheme.
From my version...
Paladin Conversion: If you were a paladin or ex-paladin before becoming a bone knight, some abilities change due to your allegiance to Karrnath and its association with the undead. You can no longer detect evil. The ability to Smite Evil changes to smiting known enemies of Karrnath or anyone acting in a manner that would cause harm to Karrnath. You can use your Lay on Hands ability to heal both living and undead creatures.
The lay on hands change is to allow the paladin to continue being able to heal himself. Likewise the change I made to channel energy is that it becomes negative energy, though because of the undead association the Bone Knight can always heal himself with the negative energy from his own channel.
I think you have the right idea with the skeletal steed/weapon bond. You choose one or the other as per normal paladin progression. Changing "holy" to "unholy" was the only original change I made to the weapon bond of the Bone Knight but the anti-paladin enhancements seem fairly appropriate.
Hope this helps.