/u/Glide08
Suharno did promulgate a vision for Maphilindo in the 1960s period, comprising Malaysia, Philippines, and Indonesia. As far as I know there was no mention of claims toward PNG. Sukarno's vision evolved over time.
At the start of the 20th century, there were arguments for a united "greater Indonesia" or "greater Malaysia" that was to comprise today's Indonesia, Malaysia, Singapore, Brunei, etc. Throughout I will use the term "Greater Indonesia", "Greater Malaysia" and "Greater Malaya" interchangeably as the intent is clear. Among others, the idea of a Greater Malaya was promoted by Ibrahim bin Haji Yaacob, a then-British Malaya-based pan-Malay politician who founded the Kesatuan Melayu Muda (KMM) or Young Malays Union in the 1920s-30s, around the time that nationalist movements were starting to form both in the British and Dutch colonies of SE Asia. KMM embraced Japan's invasion and occupation of SE Asia, expecting the Japanese to make moves toward setting up for independence.
However, similarly to the experience of many nationalist groups in Indonesia such as Sarekat Islam and Sukarno's own Partai Nasional Indonesia, the KMM discovered that the Japanese were in no hurry to grant much independence at all. However, the Japanese significantly re-organized the administration of SE Asia, violating previous partitions due the British and the Dutch: the Japanese placed Sumatra and the Malay peninsula under the 25th Army, Java and Madura under the 16th Army, and Borneo along with eastern parts of Indonesia were under the 2nd South Fleet of the Navy. Borneo was considered a vital area as it provided many key strategic resources to the IJN.
As WW2 went poorly for the Japanese, they started to promise the idea of independence in the future in exchange for collaboration.
The Japanese allows the creation of auxiliary volunteer militia units in SE Asia that could be used a nucleus for a nationalist army to guarantee their independence lest the European colonial powers return something that Sukarno bought into.
Mere days after Japanese surrender, on 17 August 1945, Sukarno and Hatta proclaimed the independence of "Indonesia" without specifying what exactly it was, in the very short proclamation avoiding the use of the term Indonesia Raya even if the national anthem uses it as the title. Within days and weeks, Allied units started to land in Java and the battle for the independence of Indonesia had began.
In the 1945-1959 period, Sukarno himself made little reference to "Greater Indonesia" in any way. In fact, in 1945-49 they distanced themselves from Yaacob, as they both followed a policy of appeasement against Communists in SE Asia, who were the only party left at this point who strongly espoused the idea of "Greater Indonesia" or "Greater Malaya". This perceived anti-Communist stance is what convinced the US to pressure the Dutch to allow Indonesian independence, as they feared continuing warfare would only strengthen Communism in SE Asia.
Of course, Sukarno's own politics changed significantly in the 1950s-1960s, in particular his view of the British plans for Malays, which he claimed is a puppet state of the British. This led to Konfrontasi in the early 1960s, an undeclared war between Indonesia and Malaya. By this point Indonesia was getting significant military and economic assistance from the USSR and funneled direct and indirect aid to insurgents in Malaya, with infiltration by irregulars from Indonesia.
However, at this point Sukarno did not use the Indonesia Raya slogan, rather he used the idea of Maphilindo that included not only Indonesia and Malaya, but also the Philippines, whom he was courting as an ally in the confrontation. He also made no direct claim on northern Borneo, for he did not want to be perceived as an expansionist leader. Despite open attacks starting in 1963, the declaration of independence of Malaya which included northern Borneo went ahead.
In 1965, Sukarno himself was deposed and replaced with the pro-US Suharto, and relationship between Indonesia and Malaya was normalized.
Southeast Asian Culture and Heritage in a Globalising World, by Ooi Giok Ling, Rahil Ismail, Brian B. Shaw.
The Politics of Indonesia-Malaysia Relations: One Kin, Two Nations, by Joseph Chinyong Liow.