The 'author' of this interesting remark would appear to be Catherine Charlotte de Gramont (1639-1738) who was Princess of Monaco as the wife of Louis I of Monaco.
The Princesse de Monaco, who was generous with her favors, was heard
to remark gaily of Louis’s penis that, although his power was great,
his scepter was very small, unlike that of his cousin Charles of
Source: Lisa Hilton, 'Athenais: The Life of Louis XIV's Mistress, the Real Queen of France'
The attribution to the Princess of Monaco also appears in a 2015 article in Le Point
Après quelques accouchements, direction Paris où elle
décroche une place d’honneur dans la suite d’Henriette d’Orléans,
l’épouse du frère du roi.... si l’on en croit le compte rendu de la princesse
de Monaco elle-même, qui affirmait que la puissance du roi était
grande, "mais son sceptre tout petit, contrairement à son cousin
Translation: After a few deliveries [i.e. the births of her children with Louis I], she went to Paris where she landed a place of honor in the suite of Henriette d'Orléans, the wife of the king's brother.... the account of the Princess of Monaco herself, who claimed that the power of the king was great, "but his sceptre is very small, unlike his cousin Charles of England".
Catherine-Charlotte de Gramont. Public domain
Catherine-Charlotte de Gramont was Louis XIV's mistress for a few months in 1666 and / or 1667; the affair ended when Catherine's ongoing liaisons with her cousin, Antoine Nompar de Caumont (comte de Puyguilhem), and Armand de Gramont (comte de Guiche) threatened to embroil the French king in more scandal than even the court at Versailles could handle. However, while Catherine's observations on Louis XIV's 'sceptre' came from personal experience, there does not appear to be any evidence that she ever had affair with Charles II of England. It's not hard to imagine, though, that she picked this up from court gossip and, perhaps used it spitefully (as noted below by LangLangC's citation of Antonia Fraser) when she was banished from the court in 1668 for yet another affair.
As LangLangC has pointed out in a comment below, this is hearsay - but that may well be all we have. Neither of two contemporary sources, The memoirs of the Duke of Saint-Simon on the reign of Louis XIV and the regency nor the three volume Memoirs of Mademoiselle de Montpensier (vol. 1, vol. 2, vol. 3) make any mention of this quote.
The Princess' supposed remark is mentioned in Jean Teulé's 2008 historical novel Le Montespan, a copy of which can be downloaded for free here. The book won the Grand Prix du roman historique, though presumably more for its literary merits than historical accuracy.