Both properties were used to run his drug empire that the Crown says included selling more than 1.682 kilograms of methamphetamine while police were intercepting his conversations.
Crown lawyer Jacinda Foster said the money should entitle Gray to four years off his sentence.
But Gray's lawyer Philip Morgan QC said the $2.7m of assets entitled his client to a discount of half his end sentence.
Justice John Priestley said that created an "imposition".
He said in some criminal cases, wealthy people were able to offer large sums of money as reparation payments and, as a result, were given time off their sentence.
"One difficulty the court has is to award one standard of justice for the rich who have assets and one standard for the poor who can't make a reparation order ... Isn't there a serious risk that for serious drug offending sentences there may be an undesirable precedent for ones that are well-heeled?"
Mr Morgan said the money being handed to the Crown as part of the "instrument forfeiture" was not money made from the drug dealing.
"The taking away of money - the point to be made about it is - it is a punishment ... it does meet, in particular, the key Sentencing Act principles of deterrence and denunciation."
Justice Priestley said he was aware of the problems and "there was no easy answer."
When the judge asked how much discount Gray should be given for the 2.7m, Mr Morgan answered "half".
He said the desire for money was what motivated Gray, so a discount off his sentence of 20 per cent or 25 per cent was not meaningful.
Ms Foster earlier told the court that the properties that Gray is giving up were an "integral part" of his offending.
They were isolated, and made it possible for Gray to avoid detection.
But once police caught up with Gray and intercepted his conversations, they discovered a huge drug-ring.
Ms Foster said some of Gray's deals were in 10 ounce lots - or more than 280g.
In one of the conversations, Gray was heard to say: "f*** the little things, mate. The little things get you in the sh**. Big things come along."
He also boasted of selling 26 ounces in one week, although Mr Morgan said those figures referred to money and not drugs.
That will be just one of the questions Justice Priestley has to decide before sentencing Gray tomorrow.
Instrument forfeiture:
*A $3m farm will be sold, with $1.2m being returned to Gray.
*A $900,000 home on Hamilton's rural fringe
*Two cars worth $45,000 each
Asset forfeiture:
*$2.4m will be paid to the Crown, of which $1.29m will come from Gray's share of the farm.
