What is the rarest Tomy/Plarail/TrackMaster item you own?

Rarest in what range? That is the question.

For us, we know that:

1959-1964: パノラマトンネル. There are 2 types. Both are the very first Plarail scene parts where only 2 original packaging remains in this world. Clear images of packaging do not exist. Also Point Rail (Tentative name), it looks like a Y shaped rail but it is not and it existed in 1950.
1965-1969: 電動プラレール電車セットNO.1 & NO.2. NO.1 was just unexcavated last year and NO.2 set's existence is unconfirmed at the moment.
1970-1974: D-51きしゃセット and ちょうとっきゅうひかりごうニューセット. The same one listed above. First set was unexcavated in 2018, second set unexcavated just last year and only 1 catalogue lists these 2 sets together. That catalogue was excavated 4 months after the second set's discovery. Tough debate to include white home version of ふくせんプラレールステーションセット and 全自動ふみきりセット.
1973-1974: Single item C12ロータリーじょせつしゃ. Listed in the 1974 catalogue but the existence of single items are unconfirmed till today. Also single item slippery turnout rail, out of print 5 months after initial manufacture. Tough debate to include ハイウエィふみきりステーションセット.
1975-1979: Single item ぼくじょうふみきり. Listed in 1975 catalogue but packaging/box is unconfirmed till today. Also single item C-62汽笛入り, the amount of surviving boxes are estimated less than 4 in the world. Also the 2 types of 近郊型でんしゃふみきりえきセット, amount of survivors are less than 6 today. Tough debate to include ふえふきはっしゃセット and ニチイチェーンよいこシリーズ specification of the D-51きゅうこうれっしゃセット.
1980-1984: 福岡市交通局の地下鉄, blue box version is unnumbered EC box type and 1 survivor remains today. 京阪神通勤特急　基本Ｎｏ.３セット, 1 of the Plarail spoken about in biggest rumors and only 3 confirmed survivors remain today. Chitose Airport Set, the same rumour as above but existence unconfirmed.

Generally speaking it is extremely difficult to directly judge which one is rarer than the other provided you specify a range.

This ^
I totally agree but you might consider these.
1959-1964: ハイウェイバスセット, there are no surviving boxes found to this day but the catalogue images are confirmed.
1965-1970: 電車（青）, sakura trees and transparent blue trees, its existence is said to be a miracle as there are no images of them except the sakura trees in the catalogue and the surviving amount of trees are less than 20 in the world. The only confirmed owner of the transparent blue trees today is Mie Battery Railway.
1965-1970: プラレール部品ハウスブロック, the entire set was part of Project X Story and no one knows the DVD version contents of Project X Story till today. There are only 2 surviving sets today.
1971-1975: Single item ハウスブロック, released after Project X Story but the amount of survivors in brand new are unconfirmed today (probably none left?). D51きしゃ（青）could be considered too, I heard there is less than 50 survivors in the world.
1984: メロディーD51セット, it is a miracle that the amount of brand new survivors are less than 3 today. There are 3 types of melodies, and I don't even know if the 2 confirmed survivors have the same melody or not.