We present cosmological ($30-400$ Mpc) distributions of neutral hydrogen (HI) in the inter-galactic medium (IGM) traced by Ly$alpha$ Emitters (LAEs) and QSOs at $z=2.1-2.5$, selected with the data of the on-going Hobby-Eberly Telescope Dark Energy Experiment (HETDEX) and the eBOSS survey. We investigate spatial correlations of LAEs and QSOs with HI tomography maps reconstructed from HI Ly$alpha$ forest absorption in the spectra of background galaxies and QSOs obtained by the CLAMATO survey and this study, respectively. In the cosmological volume far from QSOs, we find that LAEs reside in regions of strong HI absorption, i.e. HI rich, which is consistent with results of previous galaxy-background QSO pair studies. Moreover, there is an anisotropy in the HI-distribution plot of transverse and line-of-sight distances; on average the HI absorption peak is blueshifted by $sim 200$ km s$^{-1}$ from the LAE Ly$alpha$ redshift, reproducing the known average velocity offset between the Ly$alpha$ emission redshift and the galaxy systemic redshift. We have identified a $sim$ 40-Mpc scale volume of HI underdensity that is a candidate for a giant HII bubble, where six QSOs and an LAE overdensity exist at $left < z right > =2.16$. The coincidence of the QSO and LAE overdensities with the HI underdensity indicates that the ionizing photon radiation of the QSOs has created a highly ionized volume of multiple proximity zones in a matter overdensity. Our results suggest an evolutionary picture where HI gas in an overdensity of galaxies becomes highly photoionized when QSOs emerge in the galaxies.
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