His comments come as parties ramp up campaigning with less than a week to go before voters head to the polls on Thursday to decide who will represent them on local councils.
Speaking to The Steamie, The Scotsman’s political podcast, the polling expert predicted local elections would potentially see SNP gains and Conservative losses, with Scottish Labour potentially sneaking into second place.
Despite the Scottish Government being under immense pressure around its competency, Sir John said issues such as the ferries fiasco would be unlikely to change many voters’ minds on who to vote for due to the pull of the constitutional debate.
Two ferries, hulls 801 and 802, are at least £150 million over budget and five years late after ministers awarded their construction contract to Ferguson Marine.
The professor of politics at Strathclyde University said the independence movement was unlikely to suffer from perceived SNP incompetence due to the possibility the party may “not survive the experience” of Scotland becoming independent.
He said: "If Scotland were to become an independent country, there is no guarantee that the SNP would inherit the earth.
"It’s just to make the point that attempting to, as it were, tar the independence brush with the incompetence of the SNP is not necessarily certainly a logical argument and I’m not sure if in the end it’s the one that works.”
The polling expert said said the real independence debate in a post-Brexit, post-Covid world ahead of a potential indyref2 had yet to begin.
He said: “What does matter is the quality of argument about the economic consequences of independence, Brexit etc, and that’s a debate we have still got to have north of the border.
"Neither side has addressed the fact that the argument for and against independence is a very, very different one from what it was in 2014.
"It's a much bigger, much starker, much more geo-strategic choice than it was in 2014."
Parties have spent much of the campaign claiming to voters they are the only ones who can beat either the SNP or the Conservatives.
However, Sir John said much of the rhetoric on election material has been “specious nonsense” and warned unionists could be missing a trick.
This is due to pro-independence voters being given a very strong cue to give their preferences to the Greens due to the coalition between the party and the SNP, with pro-union voters not receiving a similar tactical nudge.
Sir John said: “I have received loads of leaflets being told we are the only party here that can defeat the SNP, so you have to vote for us. The honest truth is that this is specious nonsense under the STV system.
"If you wish to beat the SNP or indeed you wish to beat the Conservatives or any other party, what you should do with your ballot paper, [it] doesn’t matter who you give your first preference to, just keep on ranking the candidates so that you put the party you really don’t like at the bottom.
"The unionists are in a sense at risk of missing a trick. If indeed the nationalist transfers operate more effectively than they did in 2017 and the unionist ones do not because voters have not been given the cue, then the unionist parties are at risk of losing out.”
Douglas Ross and Anas Sarwar have both indicated they are confident their respective parties will finish in second place overall, with the Scottish Conservatives having secured second in 2017 in one of their all-time best local election results.
However, Sir John said Scottish Labour moving into second would not be due to a revival in Mr Sarwar’s party’s fortunes.
He said: “If Labour get about the equivalent of the 24 per cent of the vote that they are currently getting in the polls, that will only be a point or two up on last year.
"This is not dramatic Labour recovery. We are talking about Labour coming second because of the decline in the Conservative support, not because there is some great Anas Sarwar revival.
"That we have to bear in mind. It is Tories slip to third place, the headline, it is not Labour surge to second place.”
Sir John’s assessment comes as the Scottish Tories urged Nicola Sturgeon to confirm every gagging order for Ferguson Marine employees would be waived immediately by the Scottish Government.
Ms Sturgeon said at First Minister’s Questions on Thursday: “Nobody in the employment of Ferguson shipyard will be prevented in any way, shape or form from speaking in full to Audit Scotland.”
But Scottish Conservative shadow transport minister Graham Simpson claimed: “Insiders with specific knowledge of what went wrong with the ferries contract have been prevented from speaking out by the use of gagging orders.
“These non-disclosure agreements have prevented key employees at Ferguson Marine from talking to the Auditor General or going public with what they know.”